RetrogeneDB ID:

retro_xtro_6

Retrocopy
location
Organism:Xenopus (Xenopus tropicalis)
Coordinates:GL172899.1:929360..930488(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSXETG00000003120
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:actb
Ensembl ID:ENSXETG00000025116
Aliases:None
Description:actin, beta [Source:Jamboree;Acc:XB-GENE-490883]


Retrocopy-Parental alignment summary:






>retro_xtro_6
ATGACTGACCTCCAACTTGTACATAAGCCCGCTGTCATTTTTGATATTGGTTCGGGCAACTGCAAGGCTGGAATGTCAGG
TGAAGACTTACCAACAGCAGTAGTTCCTTCCGTAGTTGGACACTTATCAGATCGGTCAGCAATGCTAGGAGCAGGTCAGC
AGCCGTACTATGTCGGAGAAATGGCCATGAGCAAAAGAGCAATCTTAGATCTGGTTTTTCCAATCAAAGAGGGCATTGTT
AAATCTTGGGACAACATGATAAAAATCTGGAAATATTTATACAAATATGAGCTTAAAAAACCATCCAGTGAACACCCCGT
CTTTCTGACAGAGGCACCTTTAAACCCTCTTAGAAACCGGCACAAGATGGCGGAAATCTTCTTTGAAAATTTCAACGTGC
CTGCAATGTATGTGTCGCATCAAGCCAACCTGGCACTTTACGCTTCTGGCCTTACTACAGGCATTGTATTAGATGTTGGA
GCAGGTATCACCCACACTGTTGCTATTTATGACGGCGTTGCTTTACCACATGCGGTGTCCAAGCTGCCTGTGGCAGGTCG
AACCATCACTCAATATTTGATGAAGTTGCTCACAGAAAATGGTTACAACTTCATCACCGCGGCGGAGAGGGAGATTGTCC
GGGACATCAAGGAGAAACTTTGCTACATTGCATTAGATCCCAGCGCCGAATATGAAAGGAATCCAAAAGATATCACTAAA
GAATATACTCTCCCAGACGGAAATGTCATTAAGATTGACAGCCAACTCTTCCGTGCTCCAGAGGCGCTATTCTCACCCAG
TAACATTGGGCTGGAGGCCCCCGGGGTACAGGGCCTGATAAATAATATAATCCAGAAGTGCCCTATAGATATACGTCGGG
CTCTTTTAAGCAACGTTGTTTTGTCCGGAGGGTCAACTCTATTCCCTGGATTTGATGAAAGGGTTTTAAGAGAACTGGAG
AAGAAAGCACCGGACGGAGTTCAAATTAAGGTCTTAGCAGCCACAGACAGGAAGTACTCTGTTTGGATCGGTGCCTCTGT
TCTAAGCAGCATGGATTCATTCAAGGAGAATTGGATCAGGAAATCAGAATATGATGAATTTGGTCCATCCATTGTCCATC
AAAAATGA

ORF - retro_xtro_6 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.86 %
Parental protein coverage: 97.87 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIV
A...D.GSG.CKAG..G.D.P.AV.PS.VG.......M.G.GQ...YVG..A.SKR.IL.L..PI..GIV
RetrocopyAVIFDIGSGNCKAGMSGEDLPTAVVPSVVGHLSDRSAMLGAGQQPYYVGEMAMSKRAILDLVFPIKEGIV
ParentalTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASG
..WD.M.KIW......EL.....EHPV.LTEAPLNP..NR.KM..I.FE.FN.PAMYV..QA.L.LYASG
RetrocopyKSWDNMIKIWKYLYKYELKKPSSEHPVFLTEAPLNPLRNRHKMAEIFFENFNVPAMYVSHQANLALYASG
ParentalRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKL
.TTGIV.D.G.G.THTV.IY.G.ALPHA...L..AGR..T.YLMK.LTE.GY.F.T.AEREIVRDIKEKL
RetrocopyLTTGIVLDVGAGITHTVAIYDGVALPHAVSKLPVAGRTITQYLMKLLTENGYNFITAAEREIVRDIKEKL
ParentalCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTYNSIMKCD
CY.ALD...E...........K.Y.LPDG.VI.I....FR.PEALF.PS..G.E..G......N.I.KC.
RetrocopyCYIALDPSAEY--ERNPKDITKEYTLPDGNVIKIDSQLFRAPEALFSPSNIGLEAPGVQGLINNIIQKCP
ParentalVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMW
.DIR..L..N.VLSGG.T..PG...R...E....AP....IK..A...RKYSVWIG.S.L.S...F...W
RetrocopyIDIRRALLSNVVLSGGSTLFPGFDERVLRELEKKAPDGVQIKVLAATDRKYSVWIGASVLSSMDSFKENW
ParentalISKQEYDESGPSIVHRK
I.K.EYDE.GPSIVH.K
RetrocopyIRKSEYDEFGPSIVHQK

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
SRP007412_brain 0 .00 RPM 1432 .32 RPM
SRP007412_heart 0 .00 RPM 392 .88 RPM
SRP007412_kidney 0 .00 RPM 392 .88 RPM
SRP007412_liver 0 .00 RPM 735 .13 RPM
SRP007412_skeletal_muscle 0 .00 RPM 167 .37 RPM

ChIP-Seq - click to see more details

Xenopus tropicalis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_xtro_6 retrocopy.

TSS - click to see more details

Xenopus tropicalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_xtro_6 was not experimentally validated.

Retrocopy orthology:
Xenopus tropicalis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 53 parental genes, and 266 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000152383 retrocopies
retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca ENSAMEG000000066011 retrocopy
retro_amel_11,
Ailuropoda melanoleuca ENSAMEG000000160151 retrocopy
retro_amel_929,
Anas platyrhynchos ENSAPLG000000101471 retrocopy
retro_apla_2,
Bos taurus ENSBTAG000000061892 retrocopies
retro_btau_286, retro_btau_903,
Canis familiaris ENSCAFG000000160203 retrocopies
retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus ENSCJAG000000000082 retrocopies
retro_cjac_243, retro_cjac_56,
Callithrix jacchus ENSCJAG000000028853 retrocopies
retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus ENSCPOG000000121011 retrocopy
retro_cpor_361,
Cavia porcellus ENSCPOG000000134671 retrocopy
retro_cpor_60,
Dipodomys ordii ENSDORG000000100791 retrocopy
retro_dord_11,
Equus caballus ENSECAG000000159352 retrocopies
retro_ecab_271, retro_ecab_994,
Equus caballus ENSECAG000000186001 retrocopy
retro_ecab_98,
Felis catus ENSFCAG000000067881 retrocopy
retro_fcat_1613,
Felis catus ENSFCAG000000264342 retrocopies
retro_fcat_257, retro_fcat_377,
Homo sapiens ENSG000000756246 retrocopies
retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Homo sapiens ENSG0000018400910 retrocopies
retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus ENSGALG000000096211 retrocopy
retro_ggal_4,
Gallus gallus ENSGALG000000287491 retrocopy
retro_ggal_6,
Gorilla gorilla ENSGGOG0000000113318 retrocopies
retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Gorilla gorilla ENSGGOG000000140436 retrocopies
retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Macropus eugenii ENSMEUG0000001624757 retrocopies
retro_meug_1006, retro_meug_1010, retro_meug_1018, retro_meug_1042, retro_meug_105, retro_meug_1085, retro_meug_1147, retro_meug_1186, retro_meug_1200, retro_meug_1230, retro_meug_1237, retro_meug_1380, retro_meug_1414, retro_meug_1437, retro_meug_1529, retro_meug_1534, retro_meug_1557, retro_meug_1588, retro_meug_1613, retro_meug_1624, retro_meug_1654, retro_meug_1656, retro_meug_1664, retro_meug_1669, retro_meug_1708, retro_meug_1716, retro_meug_1723, retro_meug_1753, retro_meug_1763, retro_meug_18, retro_meug_1935, retro_meug_1969, retro_meug_197, retro_meug_1982, retro_meug_1991, retro_meug_2100, retro_meug_2176, retro_meug_218, retro_meug_270, retro_meug_333, retro_meug_370, retro_meug_379, retro_meug_468, retro_meug_506, retro_meug_556, retro_meug_574, retro_meug_581, retro_meug_61, retro_meug_735, retro_meug_790, retro_meug_833, retro_meug_90, retro_meug_900, retro_meug_915, retro_meug_924, retro_meug_925, retro_meug_959,
Meleagris gallopavo ENSMGAG000000039602 retrocopies
retro_mgal_5, retro_mgal_6,
Microcebus murinus ENSMICG000000148633 retrocopies
retro_mmur_23, retro_mmur_352, retro_mmur_6,
Macaca mulatta ENSMMUG000000111531 retrocopy
retro_mmul_135,
Monodelphis domestica ENSMODG000000026473 retrocopies
retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furoENSMPUG000000116101 retrocopy
retro_mputfur_279,
Mustela putorius furoENSMPUG000000166122 retrocopies
retro_mputfur_440, retro_mputfur_461,
Mus musculus ENSMUSG000000295807 retrocopies
retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Mus musculus ENSMUSG000000628257 retrocopies
retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys ENSNLEG0000001338515 retrocopies
retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys ENSNLEG000000155063 retrocopies
retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Ornithorhynchus anatinus ENSOANG000000077162 retrocopies
retro_oana_4, retro_oana_8,
Oryctolagus cuniculus ENSOCUG000000058671 retrocopy
retro_ocun_720,
Otolemur garnettii ENSOGAG000000080403 retrocopies
retro_ogar_148, retro_ogar_1808, retro_ogar_2430,
Otolemur garnettii ENSOGAG000000083481 retrocopy
retro_ogar_2637,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG0000000873511 retrocopies
retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pongo abelii ENSPPYG0000001733623 retrocopies
retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Pelodiscus sinensis ENSPSIG000000021022 retrocopies
retro_psin_25, retro_psin_4,
Pan troglodytes ENSPTRG0000001889027 retrocopies
retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Rattus norvegicus ENSRNOG0000003425410 retrocopies
retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Rattus norvegicus ENSRNOG000000367011 retrocopy
retro_rnor_715,
Sorex araneus ENSSARG000000121971 retrocopy
retro_sara_267,
Sarcophilus harrisii ENSSHAG000000126944 retrocopies
retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa ENSSSCG000000075851 retrocopy
retro_sscr_548,
Sus scrofa ENSSSCG000000283551 retrocopy
retro_sscr_389,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus ENSSTOG000000147973 retrocopies
retro_itri_149, retro_itri_1881, retro_itri_4,
Tupaia belangeri ENSTBEG000000107811 retrocopy
retro_tbel_422,
Xenopus tropicalis ENSXETG000000214171 retrocopy
retro_xtro_24,
Xenopus tropicalis ENSXETG00000025116 1 retrocopy
retro_xtro_6 ,


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