RetrogeneDB ID: retro_btau_1167

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:784985..785471(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRLS1
• Ensembl ID: ENSBTAG00000000065
• Aliases: None
• Description: cardiolipin synthase [Source:RefSeq peptide;Acc:NP_001092421]

Sequence

>retro_btau_1167
CTATGTGAAAATCCATGGACAATTCCAGATGTTTTGTGAATGAGAATTGGCTTGCCTCCAGTTTGGGGCTATTTGATTAC
CAGAGAAGATTTTCATATTGCATTACGAGTTTTTGCTTTAGCTGGTCTACTCGATTTGTTGAATGAATTTTTTGTTCAAA
ATTTGGACAATCAGAAATCAACTCTTGGATGTGTTCTTGGTTAACCTGCTGATACAATACCTATCAGTACCTTCTATATT
AGTTTGACCTATGCAGATATTATTCTGGTCTTACTTATTTACATGATAATTTTAAAGATGTAATGTTGATTGCTATGATT
TTGATGTCAAATATTGAACTCTTCCAACATTGAGAATGCTTGCTAGCTATTCCAATCCTTGCTGTGCCACTACTAAATTA
AAACCAGTTCTCATCAGCAAGGTAGACACAGAAGCCCACCTCACCTTGGTGGCAGCTTCTTTGGCAGCTGAGTTTTCAGT
TATAGT

Alignment

ORF - retro_btau_1167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.87 %
• Parental protein coverage: 54.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LYENPWTIPNMLSMTRIGLAPVLGYLIIEEDFNIALGVFALAGLTDLLDGFIARNWASQKSALGSALDPL
          L.ENPWTIP..L.M.RIGL.PV.GYLI..EDF.IAL.VFALAGL.DLL..F...N...QKS.LG..L...
Retrocopy LCENPWTIPDVL*M-RIGLPPVWGYLITREDFHIALRVFALAGLLDLLNEFFVQNLDNQKSTLGCVLG*P

Parental  ADKILISILYISLTYADLIPVPLTYMII-SRDVMLIAAV-FYVRYRTLPTPRTLSKYFNPCYATARLKPT
          AD.I.IS..YISLTYAD.I.V.L.YMII...DVMLIA...F.V.Y.TLPT.R.L..Y.NPC.AT..LKP.
Retrocopy ADTIPISTFYISLTYADIILVLLIYMII<FKDVMLIAMI<FDVKY*TLPTLRMLASYSNPCCATTKLKPV

Parental  FISKVNTAVQLILVAASLAAP-VFNYA
          .ISKV.T...L.LVAASLAA..VF.Y.
Retrocopy LISKVDTEAHLTLVAASLAAE<VFSYS

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	127.75 RPM
ERP005899_muscle	0.00 RPM	30.14 RPM
SRP017611_brain	0.00 RPM	10.37 RPM
SRP017611_kidney	0.00 RPM	17.49 RPM
SRP017611_liver	0.00 RPM	34.21 RPM
SRP030211_testis	0.00 RPM	47.91 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1167 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1167 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1167 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_930

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010596	1 retrocopy	retro_amel_1758,
Bos taurus	ENSBTAG00000000065	1 retrocopy	retro_btau_1167 ,
Canis familiaris	ENSCAFG00000005934	1 retrocopy	retro_cfam_1002,
Equus caballus	ENSECAG00000023869	2 retrocopies	retro_ecab_247, retro_ecab_930,
Felis catus	ENSFCAG00000023647	1 retrocopy	retro_fcat_1393,
Microcebus murinus	ENSMICG00000011666	1 retrocopy	retro_mmur_751,
Mustela putorius furo	ENSMPUG00000006349	1 retrocopy	retro_mputfur_1021,
Rattus norvegicus	ENSRNOG00000021273	3 retrocopies	retro_rnor_2865, retro_rnor_2866, retro_rnor_2977,