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 symbol: ITGB1BP1
• Ensembl ID: ENSBTAG00000013063
• Aliases: None
• Description: Integrin beta-1-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBM4]

Sequence

>retro_btau_1221
ATGTTTCATAAAGGAAAAAAGCACCACAGCAGTAGCAGTTCCCAGAGCAGTGAAATCAGTACCAAGAACAAGTTGGTAGA
CTCCAACCTTGGGGGGCTGTCACGGTCCAGCACCGTGGCAAGCCTCAACACCTATTCCAGCAAGAACACAGGACAAAGCA
ACAATTCAGACACCTGTGCAGAACTTCGAATAAAGTATGTTGGTACCACTGAGAAACTGAAACTTTTGGAGGGGAAAAGT
TCGAAGGACCACTGGACCTGATAAATTATATAGTTATTGCCCAGCAAGATGGAAAGTTGTCCTTTGATCCTCTGGAGGAA
GAATTTATTATGGGAGTTTCCAAGTATGGTATAAAGGCATCCACATCAGATCAATATGGTGTTCCGCATCGGCTCGCTCT
GTATTTAATCATCTGGATGGTGTGTTTCCACGATGGTCTCGAGGCAGGAAAAGAGCTTTCTGGCTCTGAAGACCACATAT
GCAAGCAACCAAGAATACAGTCTGTGGGTTTACCAGTGCAACAGCCTGGAACAAGCACAAGTAATCTGCAAAGTTTTACC
AACTGCTTTCGACTCTGTATTGACATCTGAGAAA

Alignment

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:

Parental  MFRKGKKRHSSSSSQSSEISTKSKSVDSSLGGLSRSSTVASLDTDSTKSSGQSNNNSDTCAEFRIKYVGA
          MF.KGKK.HSSSSSQSSEISTK.K.VDS.LGGLSRSSTVASL.T.S.K..GQSNN.SDTCAE.RIKYVG.
Retrocopy MFHKGKKHHSSSSSQSSEISTKNKLVDSNLGGLSRSSTVASLNTYSSKNTGQSNN-SDTCAELRIKYVGT

Parental  IEKLKLSEGKS-LEGPLDLINYIDVAQQDGKLPFVPLEEEFIMGVSKYGIKVSTSDQYDVLHRHALYLII
          .EKLKL.EGKS..EGPLDLINYI..AQQDGKL.F.PLEEEFIMGVSKYGIK.STSDQY.V.HR.ALYLII
Retrocopy TEKLKLLEGKS<FEGPLDLINYIVIAQQDGKLSFDPLEEEFIMGVSKYGIKASTSDQYGVPHRLALYLII

Parental  RMVCYDDGLGSG-KSLLALKTTDANNQEYSLWVYQCNSLEQAQAICKVLSTAFDSVLTSEK
          .MVC..DGL..G.KS.LALKTT.A.NQEYSLWVYQCNSLEQAQ.ICKVL.TAFDSVLTSEK
Retrocopy WMVCFHDGLEAG>KSFLALKTTYASNQEYSLWVYQCNSLEQAQVICKVLPTAFDSVLTSEK

Legend:

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

Expression

RNA-Seq

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

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1221 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1221 has 0 orthologous retrocopies within eutheria group .

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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	ENSCHOG00000013602	2 retrocopies	retro_chof_1385, retro_chof_432,
Callithrix jacchus	ENSCJAG00000006250	3 retrocopies	retro_cjac_1650, retro_cjac_2776, retro_cjac_393,
Dasypus novemcinctus	ENSDNOG00000008930	3 retrocopies	retro_dnov_1422, retro_dnov_2198, retro_dnov_727,
Homo sapiens	ENSG00000119185	1 retrocopy	retro_hsap_277,
Gorilla gorilla	ENSGGOG00000001754	1 retrocopy	retro_ggor_321,
Macropus eugenii	ENSMEUG00000006761	1 retrocopy	retro_meug_1434,
Microcebus murinus	ENSMICG00000002359	7 retrocopies	retro_mmur_1251, retro_mmur_1342, retro_mmur_1375, retro_mmur_1523, retro_mmur_1539, retro_mmur_244, retro_mmur_442,
Myotis lucifugus	ENSMLUG00000010629	2 retrocopies	retro_mluc_1218, retro_mluc_1752,
Macaca mulatta	ENSMMUG00000018036	1 retrocopy	retro_mmul_563,
Nomascus leucogenys	ENSNLEG00000013322	1 retrocopy	retro_nleu_1488,
Oryctolagus cuniculus	ENSOCUG00000003726	1 retrocopy	retro_ocun_120,
Otolemur garnettii	ENSOGAG00000001679	4 retrocopies	retro_ogar_1235, retro_ogar_1383, retro_ogar_2353, retro_ogar_981,
Procavia capensis	ENSPCAG00000005976	1 retrocopy	retro_pcap_241,
Pongo abelii	ENSPPYG00000012667	1 retrocopy	retro_pabe_391,
Pan troglodytes	ENSPTRG00000011637	1 retrocopy	retro_ptro_231,
Sorex araneus	ENSSARG00000009799	1 retrocopy	retro_sara_735,
Tarsius syrichta	ENSTSYG00000014537	1 retrocopy	retro_tsyr_225,
Tursiops truncatus	ENSTTRG00000000859	1 retrocopy	retro_ttru_712,