RetrogeneDB ID: retro_btau_1581

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:54075652..54076555(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000011938
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A15
• Ensembl ID: ENSBTAG00000011647
• Aliases: None
• Description: mitochondrial ornithine transporter 1 [Source:RefSeq peptide;Acc:NP_001039791]

Sequence

>retro_btau_1581
ATGAAATCCAGTCCTGCTATCCAGGCTGCCATCGACCTCACCGCGGGGGCCCTGGGGGGCACAGCGTGCGTCCTGACCGG
GCAGCCCTTCGACACTATGAAGGTGAAGATGCAGACGTTCCCCGGCCTGTACAAGGGCCTCACCGACTGTGCCCTGAAGA
CGTACTCCCAGGTGGGCTTGCGGGGCTTCTACAAGGGGACCGGCCCCGCGCTAATGGCCTACGTCGCCGAGAACTCGGTC
CTCTTCATGTGCTACGGCTTCTGCCAACATTTCGTTAGGAAAGTGGCTGGACTGGACGAGCAGGCGAAGCTGAATGATCT
GCAAACTGCGGCCGCAGGTTCCATCGCCTCAGCGTTTGCCGCGCTGGCCCTGTGCCCCACTGAGCTCGTGAAGTGCCGGC
TGCAGACCATGCACGAACTGGAGATGTCAGGGAGGATAGCCAAAAGCCATGATACAGTTTGGTCCGTCGTGAAGAGTATC
CTTAGAAAGGATGGCCCCTGGGGCTTCTACCACGGACTCACCAGTACTCTGTTTCAAGTAGTACCAGGCTATTTCTTCTT
CTTCGGTGGCTATGAACTGAGCCGATCGTTTTTTGCCTCCGGGGGTTCAAAAGATGAACTAGGCCCTGTCCCCTTGATGT
TAAGTGGTGGAATTGCTGGCATTTGCCTTTGGTTTGTCATATACCCCGTGGATTGTATCAAATCCAGAATTCAGGTTCTT
TCCATGTTTGGAAAACAGACAGGATTCATCAGAACTCTTTTAAGTGTTGTGAGAACCGAAGGAATAGCAGCTTTATATTC
TGGTCTGAAAGCTACTCTGATTCGAGCGTTTCCTGCCAATGCAGCACTATTTTTGGCTTATGAATACAGCAGGAAAATGA
TGATGAGCCAGTTTGAAGCATAT

Alignment

ORF - retro_btau_1581 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.72 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSNPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPA
          MKS.PAIQAAIDLTAGA.GGTACVLTGQPFDTMKVKMQTFP.LY.GLTDC.LKTYSQVG.RGFYKGT.PA
Retrocopy MKSSPAIQAAIDLTAGALGGTACVLTGQPFDTMKVKMQTFPGLYKGLTDCALKTYSQVGLRGFYKGTGPA

Parental  LIANIAENSVLFMCYGFCQQVVRKVVGLDRQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQTMYEM
          L.A..AENSVLFMCYGFCQ..VRKV.GLD.QAKL.DLQ.AAAGS.ASAFAAL.LCPTELVKCRLQTM.E.
Retrocopy LMAYVAENSVLFMCYGFCQHFVRKVAGLDEQAKLNDLQTAAAGSIASAFAALALCPTELVKCRLQTMHEL

Parental  ETSGKIAKSQNTVWSVVKTVFRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELGPV
          E.SG.IAKS..TVWSVVK...RKDGP.GFYHGL.STL...VPGYFFFFGGYELSRSFFASG.SKDELGPV
Retrocopy EMSGRIAKSHDTVWSVVKSILRKDGPWGFYHGLTSTLFQVVPGYFFFFGGYELSRSFFASGGSKDELGPV

Parental  PLMLSGGFGGICLWLAVYPVDCIKSRIQVLSMSGKQAGFIGTFISIVKNEGVPALYSGLKPTLIRAFPAN
          PLMLSGG..GICLW...YPVDCIKSRIQVLSM.GKQ.GFI.T..S.V..EG..ALYSGLK.TLIRAFPAN
Retrocopy PLMLSGGIAGICLWFVIYPVDCIKSRIQVLSMFGKQTGFIRTLLSVVRTEGIAALYSGLKATLIRAFPAN

Parental  GALFLAYEYSRKLMMNQFEAY
          .ALFLAYEYSRK.MM.QFEAY
Retrocopy AALFLAYEYSRKMMMSQFEAY

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	0.07 RPM	32.88 RPM
ERP005899_muscle	0.05 RPM	31.57 RPM
SRP017611_brain	0.05 RPM	11.10 RPM
SRP017611_kidney	0.00 RPM	21.75 RPM
SRP017611_liver	0.00 RPM	27.41 RPM
SRP030211_testis	3.23 RPM	3.31 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1581 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1581 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1581 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_688

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011723	1 retrocopy	retro_amel_5,
Bos taurus	ENSBTAG00000011647	1 retrocopy	retro_btau_1581 ,
Canis familiaris	ENSCAFG00000005955	1 retrocopy	retro_cfam_211,
Choloepus hoffmanni	ENSCHOG00000004899	3 retrocopies	retro_chof_1643, retro_chof_494, retro_chof_561,
Erinaceus europaeus	ENSEEUG00000014870	1 retrocopy	retro_eeur_329,
Mus musculus	ENSMUSG00000031482	1 retrocopy	retro_mmus_75,
Oryctolagus cuniculus	ENSOCUG00000016684	2 retrocopies	retro_ocun_192, retro_ocun_1927,
Ochotona princeps	ENSOPRG00000014616	1 retrocopy	retro_opri_7,
Rattus norvegicus	ENSRNOG00000011881	1 retrocopy	retro_rnor_130,
Sorex araneus	ENSSARG00000002472	1 retrocopy	retro_sara_30,
Sus scrofa	ENSSSCG00000009373	1 retrocopy	retro_sscr_688,