RetrogeneDB ID: retro_btau_1404

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:107214851..107215352(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM220
• Ensembl ID: ENSBTAG00000003958
• Aliases: None
• Description: transmembrane protein 220 [Source:RefSeq peptide;Acc:NP_001178972]

Sequence

>retro_btau_1404
ATGACGCCGGGGGCGGGGCGCAGGGCGCGGGGCCTATGGCGCGCCTGCGCCTGGCTCGTGGGCGCCTTCTTCGCGCTGGC
GGTCTTTGTGCAGGTGAACGATCCGGATGCAGAACTGTGGGTGGTTGTGTATACGATTCCTGCCACTCTGACCCTGCGTG
TTGGACTTAACCCTCTTGTCACAGGTAACTTTATTTGGAAGAGTGTGTCTGCAATACACATATTCCTTTGTGTCCTGTGG
GCTATCAGCTTGGCATACAACCTCTTGCTTCATAAGAAACAGAACCTCTTGCATGAGGAGGAAGGCAGGAAGCTGTTTGG
TCCCGTGATCATCACAGCATGGCTGGGCCTGTGCCACAGCTCTTCAAAGGCTCCAGGTGGTGGAAGAGTTCAGCTGGCCA
ATGCTACCACAGTCGCTCTTCTCCCGTTTATCTCCTAGGTCTACATATACATACACAAGGAGATGTGCTCCCCCTGGCCA
ACTCATTGCAAGACGGTGATT

Alignment

ORF - retro_btau_1404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPAAGRGARGLWRACNWLMGAFFALAAFVQVNDPDAELWVVMYTIPATLTLLVGLNPLVTGNFIWKSVS
          M.P.AGR.ARGLWRAC.WL.GAFFALA.FVQVNDPDAELWVV.YTIPATLTL.VGLNPLVTGNFIWKSVS
Retrocopy MTPGAGRRARGLWRACAWLVGAFFALAVFVQVNDPDAELWVVVYTIPATLTLRVGLNPLVTGNFIWKSVS

Parental  AIHIFLCVLWAISLAYNLLLHKKQNLLHEEEGRELFGLVIITAWLGLCHSSSKAPGGGRIQLAIATTVAF
          AIHIFLCVLWAISLAYNLLLHKKQNLLHEEEGR.LFG.VIITAWLGLCHSSSKAPGGGR.QLA.ATTVA.
Retrocopy AIHIFLCVLWAISLAYNLLLHKKQNLLHEEEGRKLFGPVIITAWLGLCHSSSKAPGGGRVQLANATTVAL

Parental  LPFISWVYIYINKEMRSSWPDHCKTVI
          LPFIS.VYIYI.KEM.S.WP.HCKTVI
Retrocopy LPFIS*VYIYIHKEMCSPWPTHCKTVI

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	139.65 RPM
ERP005899_muscle	0.05 RPM	24.39 RPM
SRP017611_brain	0.00 RPM	5.07 RPM
SRP017611_kidney	0.41 RPM	43.27 RPM
SRP017611_liver	0.00 RPM	33.22 RPM
SRP030211_testis	0.03 RPM	3.70 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1404 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1404 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1404 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003958	1 retrocopy	retro_btau_1404 ,
Echinops telfairi	ENSETEG00000015072	1 retrocopy	retro_etel_956,