RetrogeneDB ID:

retro_ecab_802

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:4:19792127..19793509(-)
Located in intron of:ENSECAG00000015372
Retrocopy
information
Ensembl ID:ENSECAG00000015879
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSECAG00000022260
Aliases:None
Description:Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:F7BQJ6]


Retrocopy-Parental alignment summary:






>retro_ecab_802
ATGGGCAAAGAGAAGACCCATATCAATACTGTCGTCATTGGCCATGTGGATCTGGCAAGTCCACCACCATCGGGCACCTC
ATCTACAAGTGTGGGGGCATTGACAAGAGAACCATCGAGAAGTTTGAGAAGGAAGCAGCAGAGATGGGCAAGGGCTCCTT
CAAGTACGCCTGGGTGCTGGACAAGCTGAAGGCAGAGAGAGAACGTGGCATCACCACAGACATCTCCCTGTGGAAGTTTG
AAACCAGCAAATACTACATCACCATCATTGATGCCCCAGGCCACAGGGATTTCATCAAGAACATGATTACTGGCACTTCC
CAGGCCGACTGCACCGTGCTCATCGTGGCCGCTGGCGTGGGCGAGTTTGAGGCTGGCATCTCCAAGAACGGGCAGACCCG
TGAGCATGCGCTACTGGCCTTTACGCTGGGTGTGAAGCAGCTCATCGTGGCTGTCAACAAGATGGACTCAACTGAGCCTG
CCTACAGCGCCGCGCGCTTCCAGGACATCACCAAGGAAGTGAGCGCCTACATCAAGAAGATCGGCTACAACCTGGCCACC
CTGGCCTTCGTGCCCATCTCGGGCTGGCACGGCGACAACATGCTGGAGCCCAGCACCAACATGCCCTGGTTCAAGGGCTG
TAAGGTGGAGAGGAAAGAGGGAAACGCCACCGGGGTGACTCTGCCGGAAGCTCTGGACTCCATCCTCCTGCCCACTCGCC
CGGTCAACAAGCCTCTGAGGCTGCCTCTGCAAGACGTGTACAAGATTGGAGGCATTGGCACTGTGCCTGTAGGCCGCGTG
GAGACCGGCTTCCTGAAACCTGGGATGGTGGTCACCTTTGCCCCCAGCAACCTCACCACCGAGGTCAAGTCTGTGGAGAT
GCACCACGAAGCCCTGACTGAGGCCCTGCCTGGTGACAACGTGGGCTTCAACGTCAAGAATGTGTCTGTGAAGGACATCC
ATCGTGGAAATGTGGCTGGAGCCAGCAAGAACGACCCCCTCATAGAGGCTGGCAGCTTTGTGGCACAGGTGATCATCTTG
AACCACCCTGGGCAGATCCACGCCGGCTATACCCCAGTGCTGGACTGCCATACAGCCCACATCTCTTGCAAGTTTGCTGA
ATTGAGGGAAAAGATTGACAGGCGCTCAGGCAAGAAGCTGGAGGAAAACCCCAGGGCCCTGAAGTCGGGCGATGCAGCGA
TGGTGCAGATGGTCCCCAGCAAGGCCATGTGTGTGGAAACTTTCTCTGAGTACCCACCTCTAGGCCGTTTTGCTTTGCGG
GACATGAGCCAAACAGTGGCTGTTGGAGTCATCAAGACAGTGGATAAGAAGTCAACCACAGCTGGCAAGGTCACCAAGTC
AGCAGTAAAGGCGAGCAAGAAG

ORF - retro_ecab_802 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.16 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMGKEKTYINIVVIGHVD-SGKSTTTGHLIYKCGGIDKRTIEKFEKEAGEMGKGSFKYAWVLDKLKAERER
MGKEKT.IN.VVIGHVD.SGKSTT.GHLIYKCGGIDKRTIEKFEKEA.EMGKGSFKYAWVLDKLKAERER
RetrocopyMGKEKTHINTVVIGHVD<SGKSTTIGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERER
ParentalGITIDISLWKFETSKYYITIIDAPGRRDFIKNVITGTSQADCAVLIVAGGVGEFEAGISKNGQTREHALL
GIT.DISLWKFETSKYYITIIDAPG.RDFIKN.ITGTSQADC.VLIVA.GVGEFEAGISKNGQTREHALL
RetrocopyGITTDISLWKFETSKYYITIIDAPGHRDFIKNMITGTSQADCTVLIVAAGVGEFEAGISKNGQTREHALL
ParentalAFTLGVKQLIVAVNKMDSTEPAYSAARFQEITKEVSAYIKKIGYNPATVAFVPISGWHGDNMLEPSSNMP
AFTLGVKQLIVAVNKMDSTEPAYSAARFQ.ITKEVSAYIKKIGYN.AT.AFVPISGWHGDNMLEPS.NMP
RetrocopyAFTLGVKQLIVAVNKMDSTEPAYSAARFQDITKEVSAYIKKIGYNLATLAFVPISGWHGDNMLEPSTNMP
ParentalWFKGWKVERKEGNATGVTLLEALDSILPPTRPVNKPLRLPLQDVYKIGGIGT-PVGRVETGFLKPGMVVT
WFKG.KVERKEGNATGVTL.EALDSIL.PTRPVNKPLRLPLQDVYKIGGIGT.PVGRVETGFLKPGMVVT
RetrocopyWFKGCKVERKEGNATGVTLPEALDSILLPTRPVNKPLRLPLQDVYKIGGIGTVPVGRVETGFLKPGMVVT
ParentalFAPSNLTTEVKSVEMHHEALTEALPGDNVGFNVKNVSVKDIHRGNVAGDSKNDPPIEAGSFVAQVIILNH
FAPSNLTTEVKSVEMHHEALTEALPGDNVGFNVKNVSVKDIHRGNVAG.SKNDP.IEAGSFVAQVIILNH
RetrocopyFAPSNLTTEVKSVEMHHEALTEALPGDNVGFNVKNVSVKDIHRGNVAGASKNDPLIEAGSFVAQVIILNH
ParentalPGQIHAGYTPVLDCHTAHISCKFAELREKIDRRSGKKLEKNPKALKSGDAAIVQMVPSKAMCVETFSEYP
PGQIHAGYTPVLDCHTAHISCKFAELREKIDRRSGKKLE.NP.ALKSGDAA.VQMVPSKAMCVETFSEYP
RetrocopyPGQIHAGYTPVLDCHTAHISCKFAELREKIDRRSGKKLEENPRALKSGDAAMVQMVPSKAMCVETFSEYP
ParentalPLGHFAVRDMRQTVAVGVIKTVDKKSSTAGKVTKSAVKASKK
PLG.FA.RDM.QTVAVGVIKTVDKKS.TAGKVTKSAVKASKK
RetrocopyPLGRFALRDMSQTVAVGVIKTVDKKSTTAGKVTKSAVKASKK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP021940_articular_cartilage 0 .00 RPM 0 .00 RPM
SRP021940_cerebellum 0 .00 RPM 0 .05 RPM
SRP021940_embryo 0 .05 RPM 0 .23 RPM
SRP021940_placental_villous 0 .00 RPM 0 .05 RPM
SRP021940_synovial_membrane 0 .00 RPM 0 .11 RPM
SRP021940_testis 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_802 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_802 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_802 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 42 parental genes, and 388 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000778614 retrocopies
retro_amel_1064, retro_amel_1072, retro_amel_1079, retro_amel_1140, retro_amel_1167, retro_amel_1203, retro_amel_1227, retro_amel_1283, retro_amel_1371, retro_amel_160, retro_amel_1742, retro_amel_1797, retro_amel_1855, retro_amel_200,
Bos taurus ENSBTAG000000145343 retrocopies
retro_btau_114, retro_btau_115, retro_btau_192,
Canis familiaris ENSCAFG000000122221 retrocopy
retro_cfam_1478,
Callithrix jacchus ENSCJAG000000100516 retrocopies
retro_cjac_1431, retro_cjac_3075, retro_cjac_34, retro_cjac_3735, retro_cjac_733, retro_cjac_97,
Cavia porcellus ENSCPOG0000000406715 retrocopies
retro_cpor_1150, retro_cpor_1162, retro_cpor_1191, retro_cpor_1256, retro_cpor_1393, retro_cpor_1492, retro_cpor_1499, retro_cpor_348, retro_cpor_381, retro_cpor_387, retro_cpor_413, retro_cpor_709, retro_cpor_891, retro_cpor_918, retro_cpor_959,
Dipodomys ordii ENSDORG000000096291 retrocopy
retro_dord_509,
Equus caballus ENSECAG000000203632 retrocopies
retro_ecab_66, retro_ecab_93,
Equus caballus ENSECAG00000022260 1 retrocopy
retro_ecab_802 ,
Erinaceus europaeus ENSEEUG000000003423 retrocopies
retro_eeur_407, retro_eeur_492, retro_eeur_625,
Echinops telfairi ENSETEG0000000423614 retrocopies
retro_etel_1189, retro_etel_1248, retro_etel_1260, retro_etel_1429, retro_etel_1436, retro_etel_1472, retro_etel_1578, retro_etel_1602, retro_etel_1682, retro_etel_1808, retro_etel_2135, retro_etel_366, retro_etel_411, retro_etel_830,
Felis catus ENSFCAG0000003097714 retrocopies
retro_fcat_1021, retro_fcat_1388, retro_fcat_1569, retro_fcat_1683, retro_fcat_1825, retro_fcat_184, retro_fcat_1915, retro_fcat_220, retro_fcat_221, retro_fcat_334, retro_fcat_515, retro_fcat_566, retro_fcat_688, retro_fcat_737,
Homo sapiens ENSG0000015650827 retrocopies
retro_hsap_1093, retro_hsap_1181, retro_hsap_1567, retro_hsap_1671, retro_hsap_190, retro_hsap_2302, retro_hsap_2455, retro_hsap_2637, retro_hsap_2712, retro_hsap_278, retro_hsap_283, retro_hsap_2896, retro_hsap_2920, retro_hsap_2967, retro_hsap_2983, retro_hsap_3239, retro_hsap_3291, retro_hsap_3314, retro_hsap_363, retro_hsap_3701, retro_hsap_3706, retro_hsap_3758, retro_hsap_3825, retro_hsap_3917, retro_hsap_4220, retro_hsap_4730, retro_hsap_989,
Gorilla gorilla ENSGGOG0000002567520 retrocopies
retro_ggor_1193, retro_ggor_1258, retro_ggor_1305, retro_ggor_1444, retro_ggor_1529, retro_ggor_20, retro_ggor_2006, retro_ggor_2021, retro_ggor_2056, retro_ggor_2066, retro_ggor_2205, retro_ggor_2526, retro_ggor_2637, retro_ggor_2826, retro_ggor_322, retro_ggor_375, retro_ggor_790, retro_ggor_860, retro_ggor_919, retro_ggor_978,
Latimeria chalumnae ENSLACG000000029521 retrocopy
retro_lcha_39,
Macropus eugenii ENSMEUG0000000501823 retrocopies
retro_meug_1067, retro_meug_110, retro_meug_1160, retro_meug_1240, retro_meug_1334, retro_meug_135, retro_meug_1421, retro_meug_1451, retro_meug_1465, retro_meug_1501, retro_meug_1662, retro_meug_1690, retro_meug_1710, retro_meug_1829, retro_meug_2023, retro_meug_2044, retro_meug_2050, retro_meug_316, retro_meug_601, retro_meug_755, retro_meug_792, retro_meug_850, retro_meug_920,
Microcebus murinus ENSMICG0000001531921 retrocopies
retro_mmur_1027, retro_mmur_1116, retro_mmur_1145, retro_mmur_1182, retro_mmur_1190, retro_mmur_12, retro_mmur_1282, retro_mmur_1316, retro_mmur_1339, retro_mmur_1343, retro_mmur_1350, retro_mmur_1568, retro_mmur_171, retro_mmur_26, retro_mmur_273, retro_mmur_49, retro_mmur_682, retro_mmur_729, retro_mmur_825, retro_mmur_877, retro_mmur_9,
Myotis lucifugus ENSMLUG0000001353724 retrocopies
retro_mluc_110, retro_mluc_1252, retro_mluc_1392, retro_mluc_1430, retro_mluc_1558, retro_mluc_1628, retro_mluc_1644, retro_mluc_1853, retro_mluc_1901, retro_mluc_1910, retro_mluc_2071, retro_mluc_2148, retro_mluc_2154, retro_mluc_2277, retro_mluc_2355, retro_mluc_2358, retro_mluc_2359, retro_mluc_2391, retro_mluc_441, retro_mluc_470, retro_mluc_677, retro_mluc_950, retro_mluc_956, retro_mluc_966,
Myotis lucifugus ENSMLUG000000167601 retrocopy
retro_mluc_1250,
Macaca mulatta ENSMMUG0000000485215 retrocopies
retro_mmul_1375, retro_mmul_1407, retro_mmul_1518, retro_mmul_1525, retro_mmul_1690, retro_mmul_1707, retro_mmul_1721, retro_mmul_1739, retro_mmul_1743, retro_mmul_1906, retro_mmul_2196, retro_mmul_2250, retro_mmul_323, retro_mmul_6, retro_mmul_848,
Monodelphis domestica ENSMODG000000185334 retrocopies
retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mustela putorius furoENSMPUG000000038166 retrocopies
retro_mputfur_1514, retro_mputfur_1643, retro_mputfur_220, retro_mputfur_502, retro_mputfur_844, retro_mputfur_862,
Mustela putorius furoENSMPUG0000000427110 retrocopies
retro_mputfur_1179, retro_mputfur_1276, retro_mputfur_1351, retro_mputfur_1394, retro_mputfur_284, retro_mputfur_355, retro_mputfur_474, retro_mputfur_678, retro_mputfur_920, retro_mputfur_973,
Mustela putorius furoENSMPUG000000082893 retrocopies
retro_mputfur_1030, retro_mputfur_609, retro_mputfur_761,
Mus musculus ENSMUSG0000003774215 retrocopies
retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Nomascus leucogenys ENSNLEG000000014766 retrocopies
retro_nleu_1492, retro_nleu_1584, retro_nleu_1754, retro_nleu_1901, retro_nleu_235, retro_nleu_829,
Nomascus leucogenys ENSNLEG000000100602 retrocopies
retro_nleu_11, retro_nleu_1489,
Ornithorhynchus anatinus ENSOANG000000049081 retrocopy
retro_oana_73,
Oryctolagus cuniculus ENSOCUG000000084813 retrocopies
retro_ocun_1102, retro_ocun_187, retro_ocun_71,
Otolemur garnettii ENSOGAG000000046308 retrocopies
retro_ogar_1067, retro_ogar_2034, retro_ogar_2329, retro_ogar_2497, retro_ogar_2583, retro_ogar_3191, retro_ogar_3270, retro_ogar_643,
Otolemur garnettii ENSOGAG0000000915210 retrocopies
retro_ogar_1215, retro_ogar_1622, retro_ogar_1779, retro_ogar_1840, retro_ogar_2281, retro_ogar_2526, retro_ogar_2557, retro_ogar_3013, retro_ogar_3046, retro_ogar_3271,
Ochotona princeps ENSOPRG000000166856 retrocopies
retro_opri_1049, retro_opri_1076, retro_opri_1197, retro_opri_298, retro_opri_325, retro_opri_383,
Pongo abelii ENSPPYG000000167771 retrocopy
retro_pabe_12,
Pan troglodytes ENSPTRG000000183471 retrocopy
retro_ptro_71,
Sus scrofa ENSSSCG000000044894 retrocopies
retro_sscr_169, retro_sscr_492, retro_sscr_612, retro_sscr_758,
Ictidomys tridecemlineatus ENSSTOG000000076874 retrocopies
retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Ictidomys tridecemlineatus ENSSTOG000000288621 retrocopy
retro_itri_1028,
Tupaia belangeri ENSTBEG0000001215151 retrocopies
retro_tbel_1084, retro_tbel_1330, retro_tbel_1373, retro_tbel_1452, retro_tbel_166, retro_tbel_1841, retro_tbel_1969, retro_tbel_1994, retro_tbel_2088, retro_tbel_2091, retro_tbel_2179, retro_tbel_2205, retro_tbel_2206, retro_tbel_2218, retro_tbel_2232, retro_tbel_2419, retro_tbel_2505, retro_tbel_259, retro_tbel_2627, retro_tbel_2718, retro_tbel_2738, retro_tbel_2758, retro_tbel_282, retro_tbel_2976, retro_tbel_3032, retro_tbel_3065, retro_tbel_3067, retro_tbel_3281, retro_tbel_3307, retro_tbel_3315, retro_tbel_338, retro_tbel_354, retro_tbel_360, retro_tbel_372, retro_tbel_3813, retro_tbel_3865, retro_tbel_3967, retro_tbel_4125, retro_tbel_4192, retro_tbel_4282, retro_tbel_4352, retro_tbel_4370, retro_tbel_4466, retro_tbel_4496, retro_tbel_4639, retro_tbel_4660, retro_tbel_4695, retro_tbel_473, retro_tbel_588, retro_tbel_620, retro_tbel_903,
Tupaia belangeri ENSTBEG0000001717016 retrocopies
retro_tbel_1335, retro_tbel_1406, retro_tbel_2677, retro_tbel_2899, retro_tbel_2966, retro_tbel_3336, retro_tbel_348, retro_tbel_3485, retro_tbel_3658, retro_tbel_3727, retro_tbel_3948, retro_tbel_4091, retro_tbel_4127, retro_tbel_4290, retro_tbel_4507, retro_tbel_4527,
Tursiops truncatus ENSTTRG0000000011419 retrocopies
retro_ttru_1020, retro_ttru_1150, retro_ttru_1196, retro_ttru_1349, retro_ttru_1351, retro_ttru_1368, retro_ttru_1384, retro_ttru_1810, retro_ttru_1861, retro_ttru_1876, retro_ttru_384, retro_ttru_390, retro_ttru_401, retro_ttru_523, retro_ttru_664, retro_ttru_698, retro_ttru_844, retro_ttru_941, retro_ttru_998,
Tursiops truncatus ENSTTRG000000018351 retrocopy
retro_ttru_993,
Vicugna pacos ENSVPAG000000076379 retrocopies
retro_vpac_369, retro_vpac_404, retro_vpac_510, retro_vpac_511, retro_vpac_523, retro_vpac_544, retro_vpac_582, retro_vpac_592, retro_vpac_606,
Drosophila melanogaster FBgn00005571 retrocopy
retro_dmel_9,


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