RetrogeneDB ID: retro_btau_596

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:39015052..39016054(-)
• Located in intron of: ENSBTAG00000009150

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PDHB
• Ensembl ID: ENSBTAG00000021724
• Aliases: None
• Description: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P11966]

Sequence

>retro_btau_596
ATGGCCATGGTTGCTGGGTTGGTGCGGAGACTCCTTGAGCAGGTCTCTGGTCTGCTGAGGAGGGGTTCCCCCAGACCACA
CTGGCCACAGTGCAGGCGACAGTTCATGAGGCTATAAATCAAGGTATGGAGGAGGAGACGGAAAGAGCTGGGAGCTATTT
CTACTTGGGGAAGAAGTTGCCCTGTACGATGGGGTTAGTCGAGGCCTGTGAGAAGAATATGGAGATAAGAGGATCATAGA
TACTCCAGTTATCTGAGTCGGGTTTTGCTGGAATTGCTGTAGGTGCAGTTCTGGCTGGGTTAAGGCCCATTTGTGAATTT
ATGCTCTTCAGTTTCTCTATGCAAGCCATTTACCAGGTTATAAACTCAGCTACCAAGACCTGTTACGCATCAGGAGGCCT
TCAGCCAGTGCCCTTAGTCTTCAGGGCGCCCAGTGGCGCCCCCACAGGCGTAGCTGCCCAACACTCCCAGTGCTTTGCTG
CCTGGTATGAGCACCTCCCAGGCTTGAAGGTGATCAGTCCCTGGAATTCAGAGGATGCAAAAGGACTTATTAAATCTGCC
ATTCAGGGTAAGTCCAGTGGTGGTGCTGGAGGGGAACTGATGTATAAAGTTCCTTTTGAACTTCCCCAGGAGCACAGTCA
AAAGATTATCTGATCCCTATAGGAAAAGCCAAACTGGAAAGGCAGGGTACACGTGCAACCATAGCTTCTCATGCAAGACC
TGTCAGCCACTGCTTAGAAGCTCAGCAGTGCTATCTAAAGAGGGACTTGAATATGAGCTGATACATCTGCAGACCATCAG
ACCGATGGACATTGAAACAAGAGAAACCAATGTCATGCAGACCAGTCACCTTGTTATTGTGGAAGGAGGCTGGTCACAGT
TGGCAGTAGGAGCTGCAATCTGTGCCAGGGTGATGGAGGGTCCTGTGTTCAATTTCCTGGATGCTCCTACAGCTCGTGTC
ACCGCCACTGAGGTCCCTAGAAGACAGATTCTAGAAGATTCT

Alignment

ORF - retro_btau_596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.4 %
• Parental protein coverage: 94.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MAVVAVLVRKPLEQVSGLLRRR-FHRTAPAALQVTVREAINQGMDEELER-DEKVFLLGEEVAQYDGAYK
          MA.VA.LVR..LEQVSGLLRR..F..T..A..Q.TV.EAINQGM.EE.ER.....FLLGEEVA.YDG...
Retrocopy MAMVAGLVRRLLEQVSGLLRRG<FPQTTLATVQATVHEAINQGMEEETER<SWELFLLGEEVALYDG---

Parental  VSRGLWKKYGDKRIIDTPI-SEMGFAGIAVGAAMAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSGGL
          VSRGL...YGDKRIIDTP..SE.GFAGIAVGA..AGLRPICEFM.F.FSMQAI.QVINSA.KT.Y.SGGL
Retrocopy VSRGL*EEYGDKRIIDTPV>SESGFAGIAVGAVLAGLRPICEFMLFSFSMQAIYQVINSATKTCYASGGL

Parental  QSVPIVFRGPNGASAGVAAQHSQCFAAWYGHCPGLKVVSPWSSEDA-KGLIKSAIRDNNPVVVLEN-ELM
          Q.VP.VFR.P.GA..GVAAQHSQCFAAWY.H.PGLKV.SPW.SEDA.K.L.....R...PVVVLE..ELM
Retrocopy QPVPLVFRAPSGAPTGVAAQHSQCFAAWYEHLPGLKVISPWNSEDA>KDLLNLPFRVS-PVVVLEG<ELM

Parental  YGVPFELPSE-AQSKDFLIPIGKAKIERQGTHVTIVAHSRPVGHCLEA-ATVLSKEGIECEVINLRTIRP
          Y.VPFELP.E.AQSKD.LIPIGKAK.ERQGT..TI..H.RPV.HCLEA...VLSKEG.E.E.I.L.TIRP
Retrocopy YKVPFELPQE<AQSKDYLIPIGKAKLERQGTRATIASHARPVSHCLEA<SAVLSKEGLEYELIHLQTIRP

Parental  MDIETIEGSVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGADVPMPYAKILEDN
          MDIET.E..VM.T.HLV.VEGGW.Q..VGA.ICAR.MEGP.FNFLDAP..RVT...VP.....ILED.
Retrocopy MDIETRETNVMQTSHLVIVEGGWSQLAVGAAICARVMEGPVFNFLDAPTARVTATEVPR--RQILEDS

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	61.57 RPM
ERP005899_muscle	0.05 RPM	40.54 RPM
SRP017611_brain	0.05 RPM	41.02 RPM
SRP017611_kidney	0.06 RPM	95.43 RPM
SRP017611_liver	0.00 RPM	32.24 RPM
SRP030211_testis	0.27 RPM	84.15 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_596 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_596 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596 ,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651, retro_tbel_3170,