RetrogeneDB ID: retro_btau_1441

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:96152813..96153121(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMCO1
• Ensembl ID: ENSBTAG00000010009
• Aliases: None
• Description: Transmembrane and coiled-coil domain-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3T0N3]

Sequence

>retro_btau_1441
ATGGCTTGAATGAAATCCTTGTTTGCAATTGGCGTTTGTTTTACTGCTCAAGTGGGAATCTTCAAGTCCATATTTGATGG
TAGAATGGTGACATGGGTCTCCTCCGACTCTGCTTTCCTTCATCTGAGGACTACCTCAAGGGAGTCTGTTGGAGGCTGAC
ACCATAGACTGTTCCACCATCTTCCTGTGTATTCTCTGCACCATGTCATTGGACAGAACATCCAGAAAATCTCAGCCTTG
CCCTTTCACAAGCTGCCACCAAGCACACAGGTGGATTTCTTGGCCCTCTGCCTCCTTCTGGCAAGTTC

Alignment

ORF - retro_btau_1441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.98 %
• Parental protein coverage: 54.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVRMKSMFAIGFCFTALMGMFNSIFDGRVVAKL-PFTPLSYIQGLSHRNLLGDDTTDCSFIFLYILCTMS
          M..MKS.FAIG.CFTA..G.F.SIFDGR.V....P.T.LS.I.GL....LL..DT.DCS.IFL.ILCTMS
Retrocopy MA*MKSLFAIGVCFTAQVGIFKSIFDGRMVTWV>PPTLLSFI*GLPQGSLLEADTIDCSTIFLCILCTMS

Parental  -IRQNIQKI-LGLAPSRAATKQAGGFLGPPPPSGKF
          .I.QNIQKI.L.LA.S.AATK..GGFLGP.PPSGKF
Retrocopy <IGQNIQKI<LSLALSQAATKHTGGFLGPLPPSGKF

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	53.21 RPM
ERP005899_muscle	0.00 RPM	49.73 RPM
SRP017611_brain	0.00 RPM	46.73 RPM
SRP017611_kidney	0.00 RPM	36.57 RPM
SRP017611_liver	0.00 RPM	48.40 RPM
SRP030211_testis	0.00 RPM	32.24 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1441 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1441 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1441 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010009	1 retrocopy	retro_btau_1441 ,
Canis familiaris	ENSCAFG00000013472	2 retrocopies	retro_cfam_1640, retro_cfam_833,
Echinops telfairi	ENSETEG00000009382	2 retrocopies	retro_etel_1552, retro_etel_570,
Macropus eugenii	ENSMEUG00000011045	2 retrocopies	retro_meug_894, retro_meug_997,
Monodelphis domestica	ENSMODG00000001335	2 retrocopies	retro_mdom_1319, retro_mdom_334,
Oryctolagus cuniculus	ENSOCUG00000008441	2 retrocopies	retro_ocun_1148, retro_ocun_1642,
Sarcophilus harrisii	ENSSHAG00000016602	1 retrocopy	retro_shar_790,