RetrogeneDB ID:

retro_btau_1221

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:3:41127031..41127625(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000008894
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ITGB1BP1
Ensembl ID:ENSBTAG00000013063
Aliases:None
Description:Integrin beta-1-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBM4]


Retrocopy-Parental alignment summary:






>retro_btau_1221
ATGTTTCATAAAGGAAAAAAGCACCACAGCAGTAGCAGTTCCCAGAGCAGTGAAATCAGTACCAAGAACAAGTTGGTAGA
CTCCAACCTTGGGGGGCTGTCACGGTCCAGCACCGTGGCAAGCCTCAACACCTATTCCAGCAAGAACACAGGACAAAGCA
ACAATTCAGACACCTGTGCAGAACTTCGAATAAAGTATGTTGGTACCACTGAGAAACTGAAACTTTTGGAGGGGAAAAGT
TCGAAGGACCACTGGACCTGATAAATTATATAGTTATTGCCCAGCAAGATGGAAAGTTGTCCTTTGATCCTCTGGAGGAA
GAATTTATTATGGGAGTTTCCAAGTATGGTATAAAGGCATCCACATCAGATCAATATGGTGTTCCGCATCGGCTCGCTCT
GTATTTAATCATCTGGATGGTGTGTTTCCACGATGGTCTCGAGGCAGGAAAAGAGCTTTCTGGCTCTGAAGACCACATAT
GCAAGCAACCAAGAATACAGTCTGTGGGTTTACCAGTGCAACAGCCTGGAACAAGCACAAGTAATCTGCAAAGTTTTACC
AACTGCTTTCGACTCTGTATTGACATCTGAGAAA

ORF - retro_btau_1221 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.09 %
Parental protein coverage: 99.5 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMFRKGKKRHSSSSSQSSEISTKSKSVDSSLGGLSRSSTVASLDTDSTKSSGQSNNNSDTCAEFRIKYVGA
MF.KGKK.HSSSSSQSSEISTK.K.VDS.LGGLSRSSTVASL.T.S.K..GQSNN.SDTCAE.RIKYVG.
RetrocopyMFHKGKKHHSSSSSQSSEISTKNKLVDSNLGGLSRSSTVASLNTYSSKNTGQSNN-SDTCAELRIKYVGT
ParentalIEKLKLSEGKS-LEGPLDLINYIDVAQQDGKLPFVPLEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLII
.EKLKL.EGKS..EGPLDLINYI..AQQDGKL.F.PLEEEFIMGVSKYGIK.STSDQY.V.HR.ALYLII
RetrocopyTEKLKLLEGKS<FEGPLDLINYIVIAQQDGKLSFDPLEEEFIMGVSKYGIKASTSDQYGVPHRLALYLII
ParentalRMVCYDDGLGSG-KSLLALKTTDANNQEYSLWVYQCNSLEQAQAICKVLSTAFDSVLTSEK
.MVC..DGL..G.KS.LALKTT.A.NQEYSLWVYQCNSLEQAQ.ICKVL.TAFDSVLTSEK
RetrocopyWMVCFHDGLEAG>KSFLALKTTYASNQEYSLWVYQCNSLEQAQVICKVLPTAFDSVLTSEK

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 .00 RPM 10 .45 RPM
ERP005899_muscle 0 .00 RPM 15 .52 RPM
SRP017611_brain 0 .00 RPM 18 .41 RPM
SRP017611_kidney 0 .00 RPM 19 .03 RPM
SRP017611_liver 0 .00 RPM 8 .76 RPM
SRP030211_testis 0 .00 RPM 53 .50 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_1221 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1221 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1221 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000013063 2 retrocopies
retro_btau_1221 , retro_btau_1435,
Choloepus hoffmanni ENSCHOG000000136022 retrocopies
retro_chof_1385, retro_chof_432,
Callithrix jacchus ENSCJAG000000062503 retrocopies
retro_cjac_1650, retro_cjac_2776, retro_cjac_393,
Dasypus novemcinctus ENSDNOG000000089303 retrocopies
retro_dnov_1422, retro_dnov_2198, retro_dnov_727,
Homo sapiens ENSG000001191851 retrocopy
retro_hsap_277,
Gorilla gorilla ENSGGOG000000017541 retrocopy
retro_ggor_321,
Macropus eugenii ENSMEUG000000067611 retrocopy
retro_meug_1434,
Microcebus murinus ENSMICG000000023597 retrocopies
retro_mmur_1251, retro_mmur_1342, retro_mmur_1375, retro_mmur_1523, retro_mmur_1539, retro_mmur_244, retro_mmur_442,
Myotis lucifugus ENSMLUG000000106292 retrocopies
retro_mluc_1218, retro_mluc_1752,
Macaca mulatta ENSMMUG000000180361 retrocopy
retro_mmul_563,
Nomascus leucogenys ENSNLEG000000133221 retrocopy
retro_nleu_1488,
Oryctolagus cuniculus ENSOCUG000000037261 retrocopy
retro_ocun_120,
Otolemur garnettii ENSOGAG000000016794 retrocopies
retro_ogar_1235, retro_ogar_1383, retro_ogar_2353, retro_ogar_981,
Procavia capensis ENSPCAG000000059761 retrocopy
retro_pcap_241,
Pongo abelii ENSPPYG000000126671 retrocopy
retro_pabe_391,
Pan troglodytes ENSPTRG000000116371 retrocopy
retro_ptro_231,
Sorex araneus ENSSARG000000097991 retrocopy
retro_sara_735,
Tarsius syrichta ENSTSYG000000145371 retrocopy
retro_tsyr_225,
Tursiops truncatus ENSTTRG000000008591 retrocopy
retro_ttru_712,


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