RetrogeneDB ID: retro_btau_1362

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:96267109..96267810(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000002008
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.66194
• Ensembl ID: ENSBTAG00000016263
• Aliases: SLC25A14, BMCP-1, UCP5
• Description: brain mitochondrial carrier protein 1 precursor [Source:RefSeq peptide;Acc:NP_001039610]

Sequence

>retro_btau_1362
GAGGTGAGCATGTCGGCCCTGAAGCCCTTGGTGTATGGAGGCCTGGCCTCCATCAAGGTGGAGCGCAGTACCTTTCCAAT
TGATTTAACCAAGACACGGCTTCAGATTCAAGGCCCGAAGAACGATGCAAACTTTAAAGAAATCAGGTATGGAGGAATGT
TGCATGTATTAGTGAGGATAGGCAGAGAGGAAGGCCCGAAAGCACTATATTCGGGGATTGCCCCAGCGATGTTACACCAG
GTTTCCTATGGCACCATCAAGATAGACACCTATCAGAGCTTGAAGTGGTTATTTGTCGAGCGTCCAGAAGATGAAACCCT
TCTGATAAATGTGGTCTGTGGGATTCTCTGGAGTCATATCCTCAAGCATTGTTAATCCAACAGATGTTTTGAAGATATGA
ATGCAAGCTAAAGCAACACCCTGCAAGGAGGAATGATAGGCAACTTCATTAACATTTACCAGAAAGAGGGAAAGACAGGA
CTGTGGAAGGGCATATCCTTACCGCTCAGAGGGCTGCTACTATGGGCTTCGTGGAGCTGCCGGTCTACAGCCTCACCAAG
AAGCATCTGATTCTCTCAGGCCTGATGGGAGACACTGTGTATACCCATTTCCTCTCAAGCTTCACCTGTGGGCTGGCAGG
AGCCCTGGCCTCAAACCCTGTCAATATGTTGAGAACATGTACGATGAATCAGAGAGTCCTC

Alignment

ORF - retro_btau_1362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.81 %
• Parental protein coverage: 72.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EMSGLNWKPFVYGGLASIVAEFGTFPVDLTKTRLQVQGQSIDVRFKEIKYRGMFHALFRIYKEEGVLALY
          E.S....KP.VYGGLASI..E..TFP.DLTKTRLQ.QG...D..FKEI.Y.GM.H.L.RI..EEG..ALY
Retrocopy EVSMSALKPLVYGGLASIKVERSTFPIDLTKTRLQIQGPKNDANFKEIRYGGMLHVLVRIGREEGPKALY

Parental  SGIAPALLRQASYGTIKIGIYQSLKRLFVERLEDETLLINMICGVV-SGVISSAIANPTDVLKIRMQAQ-
          SGIAPA.L.Q.SYGTIKI..YQSLK.LFVER.EDETLLIN..CG.......SS...NPTDVLKI.MQA..
Retrocopy SGIAPAMLHQVSYGTIKIDTYQSLKWLFVERPEDETLLINVVCGIL>GVISSSIV-NPTDVLKI*MQAK<

Parental  GSLFQGSMIGSFIDIYQQEGTRGLWRGV-VPTAQRAAIVVGVELPVYDITKKHLILSGLMGDTILTHFVS
          ....QG.MIG.FI.IYQ.EG..GLW.G....TAQRAA....VELPVY..TKKHLILSGLMGDT..THF.S
Retrocopy SNTLQGGMIGNFINIYQKEGKTGLWKGI<ILTAQRAATMGFVELPVYSLTKKHLILSGLMGDTVYTHFLS

Parental  SFTCGLAGALASNPVDVVRTRMMNQRAI
          SFTCGLAGALASNPV...RT..MNQR..
Retrocopy SFTCGLAGALASNPVNMLRTCTMNQRVL

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	1.73 RPM
ERP005899_muscle	0.00 RPM	1.06 RPM
SRP017611_brain	0.00 RPM	15.67 RPM
SRP017611_kidney	0.00 RPM	2.67 RPM
SRP017611_liver	0.00 RPM	1.74 RPM
SRP030211_testis	0.00 RPM	8.96 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1362 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1362 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1362 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016263	1 retrocopy	retro_btau_1362 ,
Canis familiaris	ENSCAFG00000018766	1 retrocopy	retro_cfam_1359,
Callithrix jacchus	ENSCJAG00000002456	1 retrocopy	retro_cjac_2257,
Homo sapiens	ENSG00000102078	1 retrocopy	retro_hsap_2954,
Macaca mulatta	ENSMMUG00000008386	1 retrocopy	retro_mmul_1943,
Nomascus leucogenys	ENSNLEG00000015318	1 retrocopy	retro_nleu_1638,
Pongo abelii	ENSPPYG00000020715	2 retrocopies	retro_pabe_2450, retro_pabe_3595,
Pan troglodytes	ENSPTRG00000022268	1 retrocopy	retro_ptro_2048,
Tursiops truncatus	ENSTTRG00000016206	2 retrocopies	retro_ttru_1159, retro_ttru_1570,