RetrogeneDB ID: retro_btau_420

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:10727859..10728255(-)
• Located in intron of: ENSBTAG00000015441

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM126B
• Ensembl ID: ENSBTAG00000020596
• Aliases: None
• Description: None

Sequence

>retro_btau_420
AAGGTTAAACATGATGCTTTGAAGACATATGCATCATTGACTCTACTTCCATTTTTGTCCACTACAGTTTCCTACAGGCT
TCTTATAACAGATGCTTTGTATTTAGGTAATACAAGCCAGGAAAACTGTGTTCTGAGAAGTTCACTGATTGGCATGGCAT
GTGGTGTTTTATACCCCACTGCTTTGGCTTTTTATAAAAATGGATGTCTGGCAGTCAAGTATACTGTTCCATTACCACCA
AAAGGAAGGGTTTTATTTTACTGGCTGCTGCCTTGTCAAACAGAGATAAAAGCAATGGTGATTCCTCTCATTTTCCAGAC
AGTCTTTGGGATAGTTCATGGTTTTCAGCATTATGCAATATTTGAAAGTACATTTGAGAAAACTGTGTGTGAAGAT

Alignment

ORF - retro_btau_420 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.95 %
• Parental protein coverage: 57.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVTHDVLKTYASLTALPFLSTIVSYKLLVTDALCSGNISQENCVLRSSLIGIACGVLYPTALAFSKNGRL
          KV.HD.LKTYASLT.LPFLST.VSY.LL.TDAL..GN.SQENCVLRSSLIG.ACGVLYPTALAF.KNG.L
Retrocopy KVKHDALKTYASLTLLPFLSTTVSYRLLITDALYLGNTSQENCVLRSSLIGMACGVLYPTALAFYKNGCL

Parental  AFKYHTVPMPPKGRVLLYWLLLCHTEIKAMVIPLILQTTFGICHGLQHYAIFESTLEKTVHED
          A.KY.TVP.PPKGRVL.YWLL.C.TEIKAMVIPLI.QT.FGI.HG.QHYAIFEST.EKTV.ED
Retrocopy AVKY-TVPLPPKGRVLFYWLLPCQTEIKAMVIPLIFQTVFGIVHGFQHYAIFESTFEKTVCED

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	15.43 RPM
ERP005899_muscle	0.00 RPM	8.29 RPM
SRP017611_brain	0.00 RPM	5.02 RPM
SRP017611_kidney	0.00 RPM	10.55 RPM
SRP017611_liver	0.00 RPM	8.99 RPM
SRP030211_testis	0.12 RPM	6.85 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_420 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_420 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_420 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000451	2 retrocopies	retro_btau_1849, retro_btau_223,
Bos taurus	ENSBTAG00000020596	1 retrocopy	retro_btau_420 ,
Echinops telfairi	ENSETEG00000008939	1 retrocopy	retro_etel_200,
Mus musculus	ENSMUSG00000030614	1 retrocopy	retro_mmus_1618,
Oryctolagus cuniculus	ENSOCUG00000016529	3 retrocopies	retro_ocun_1656, retro_ocun_1671, retro_ocun_607,
Sus scrofa	ENSSSCG00000014905	1 retrocopy	retro_sscr_452,