RetrogeneDB ID:

retro_btau_192

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:18:2952295..2953684(+)
Located in intron of:ENSBTAG00000015669
Retrocopy
information
Ensembl ID:ENSBTAG00000034185
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1A1
Ensembl ID:ENSBTAG00000014534
Aliases:None
Description:Elongation factor 1-alpha 1 [Source:UniProtKB/Swiss-Prot;Acc:P68103]


Retrocopy-Parental alignment summary:






>retro_btau_192
ATGGGAAAGGAGAAGACCCACATCAACATCATTGTCATTGGGCACGTAGATTCAGGGAAGTCTACCACGACTGGCCATCT
GATCTACAAATGTGGCGGGATCGACAAGAGAACAATTGAAAAGTTCGAGAAGGAGGCTGCCGAGATGGGAAAGGGCTCCT
TCAAATATGCCTGGGTCTTGGACAAACTTAAAGCTGAACGTGAGCGTGGTATCACCATTGATATCTCCCTGTGGAAATTT
GAGACCAGCAAGTACTATGTTACCATCATTGATGCCCCAGGACACAGAGACTTCATCAAAAACATGATTACAGGCACATC
CCAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCCGGTATCTCCAAGAACGGGCAGACCC
GTGAGCATGCCCTTTTGGCTTACACCCTGGGTGTGAAACAACTAATTGTTGGCGTTAACAAAATGGATTCCACTGAGCCA
CCCTATAGCCAGAAGAGATACGAAGAAATTGTTAAGGAAGTCAGCACCTATATTAAGAAAATTGGCTACAACCCCGACAC
AGTAGCATTTGTGCCAATTTCTGGCTGGAATGGTGACAACATGCTAGAACCAAGTGCTAATAAGCCATGGTTCAAGGGAT
GGAAAGTCACCCGTAAGGACGGCAATGCCAGTGGAACCACCCTGCTTGAAGCTCTGGATTGCATTCTGCCACCAACTCGC
CCAACTGACAAACCCTTGCGTTTGCCTCTCCAGGATGTCTATAAAATTGGTGGTATTGGTACTGTCCCTGTGGGTCGTGT
GGAGACTGGTGTTCTCAAACCTGGCATGGTGGTCACCTTTGCTCCAGTCAATGTAACAACTGAAGTGAAGTCTGTAGAAA
TGCACCATGAAGCATTGAGTGAAGCCCTTCCTGGGGACAATGTGGGCTTTAATGTCAAGAACGTGTCTGTCAAAGATGTC
CGTCGTGGCAATGTGGCTGGTGACAGCAAAAATGATCCACCCATGGAAGCTGCTGGCTTCACAGCTCAGGTGATTATTTT
GAACCATCCAGGCCAAATCAGTGCTGGATATGCACCTGTGCTGGATTGTCACACAGCTCACACTGCTTGCAAGTTTGCTG
AGCTGAAGGAGAAGATTGATCGTCGTTCTGGGAAAAAGCTGGAAGATGGCCCTAAATTCTTGAAATCTGGTGACACTGCC
ATCGTTGATATGGTTCCTGGCAAGCCCATGTGTGTCGAGAGCTTCTCTGATTATCCTCCCCTGGGCCGTTTTGCTGTGCG
TGACATGAGACAGACAGTCGCTGTGGGTGTCATCAAAGCAGTGGACAAGAAGGCAGCTGGAGCTGGCAAGGTCACCAAGT
CTGCCCAGAAAGCTCAGAAGGCTAAATGA

ORF - retro_btau_192 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.13 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
MGKEKTHINI.VIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
RetrocopyMGKEKTHINIIVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
ParentalITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
RetrocopyITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
ParentalYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPW
YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSAN.PW
RetrocopyYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANKPW
ParentalFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF
FKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF
RetrocopyFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF
ParentalAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP
APVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP
RetrocopyAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP
ParentalGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPP
GQISAGYAPVLDCHTAH.ACKFAELKEKIDRRSGKKLEDGPKFLKSGD.AIVDMVPGKPMCVESFSDYPP
RetrocopyGQISAGYAPVLDCHTAHTACKFAELKEKIDRRSGKKLEDGPKFLKSGDTAIVDMVPGKPMCVESFSDYPP
ParentalLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
LGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
RetrocopyLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK

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
ERP005899_liver 0 .65 RPM 1004 .30 RPM
ERP005899_muscle 3 .54 RPM 7335 .41 RPM
SRP017611_brain 0 .37 RPM 631 .15 RPM
SRP017611_kidney 1 .19 RPM 2172 .48 RPM
SRP017611_liver 0 .68 RPM 1473 .77 RPM
SRP030211_testis 2 .23 RPM 1056 .30 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_192 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_192 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_192 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 149 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000014534 3 retrocopies
retro_btau_114, retro_btau_115, retro_btau_192 ,
Canis familiaris ENSCAFG000000132491 retrocopy
retro_cfam_1007,
Dipodomys ordii ENSDORG000000096291 retrocopy
retro_dord_509,
Equus caballus ENSECAG000000203632 retrocopies
retro_ecab_66, retro_ecab_93,
Equus caballus ENSECAG000000222601 retrocopy
retro_ecab_802,
Erinaceus europaeus ENSEEUG000000003423 retrocopies
retro_eeur_407, retro_eeur_492, retro_eeur_625,
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,
Loxodonta africana ENSLAFG000000280811 retrocopy
retro_lafr_651,
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,
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,
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,
Oryctolagus cuniculus ENSOCUG000000084813 retrocopies
retro_ocun_1102, retro_ocun_187, retro_ocun_71,
Ochotona princeps ENSOPRG000000166856 retrocopies
retro_opri_1049, retro_opri_1076, retro_opri_1197, retro_opri_298, retro_opri_325, retro_opri_383,
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,
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,
Drosophila melanogaster FBgn00005571 retrocopy
retro_dmel_9,


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