RetrogeneDB ID: retro_btau_1811

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:42130128..42131025(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000033749
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.52359
• Ensembl ID: ENSBTAG00000021991
• Aliases: None
• Description: tomoregulin-1 precursor [Source:RefSeq peptide;Acc:NP_001192405]

Sequence

>retro_btau_1811
ATGGGCGCCGTGGCCGCTGAGGCGCCGCTCCGGCTGCCGGCCGCGCCCCCGCTCGCCTTCTGCTGCTACACGTCGGTGCT
TCTGCTCTTCGCCTTCTCTCTGCCCGGGAGCCGCGCGTCCAACCAGCCCCCGGGTGGCGGCGGCGGCGGGGACTGTCCGG
GCGGCAAAGGCAAGAGCGTCAACTGCTCAGAATTAAATGTGAGGGAATCTGATCTAAGAGTTTGTGATGAATCATCATGT
AAATATGGAGGCGTCTGTAAAGAAGATGGAGATGGTTTGAAATGTGCATGTCAGTTTCAGTGCCATACGAATTACATTCC
TGTCTGTGGATCAAATGGGGACACGTACCAAAATGAATGCTTTCTCAGAAGGGCTGCTTGTAAGCACCAGAAAGAGATAA
CAGTAGTAGCGAGAGGACCGTGCTACTCTGATAATGGCTCTGGATCTGGAGAAGGAGCAGAAGAAGAAGGGTCAGGGGCA
GAAGTTCACAGAAAACACTCCAAGTGTGGACCCTGCAAGTATAAAGCTGAATGTGATGAAGATGCAGAAAATGTTGGGTG
TGTATGTAATATAGATTGCAGTGGATACAGTTTTAATCCTGTGTGTGCTTCTGATGGGAGTTCCTATAACAATCCCTGTT
TTGTTCGAGAAGCATCTTGTATAAAACAAGAACAAATTGATATAAGGCATCTTGGTCATTGCACAGACACAGATGACACT
AGTTTGTTGGGAAAGAAGGATGATGGACTACAGTATCGACCAGATGTGAAAGATGCTAGTGATCAAAGGGAAGATGTTTA
TATTGGAAACCACATGCCTTGCCCTGAAAACCTCAATGGTTACTGCATCCATGGAAAATGTGAATTCATTTATTCTACTC
AGAAGGCTTCTTGTAGA

Alignment

ORF - retro_btau_1811 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.67 %
• Parental protein coverage: 78.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGAVAAEAPLRLPAAPPLAFCCYTSVLLLFAFSLPGSRASNQPPGGGGGGDCPGGKGKSINCSELNVRES
          MGAVAAEAPLRLPAAPPLAFCCYTSVLLLFAFSLPGSRASNQPPGGGGGGDCPGGKGKS.NCSELNVRES
Retrocopy MGAVAAEAPLRLPAAPPLAFCCYTSVLLLFAFSLPGSRASNQPPGGGGGGDCPGGKGKSVNCSELNVRES

Parental  DLRVCDESSCKYGGVCKEDGDGLKCACQFQCHTNYIPVCGSNGDTYQNECFLRRAACKHQKEITVVARGP
          DLRVCDESSCKYGGVCKEDGDGLKCACQFQCHTNYIPVCGSNGDTYQNECFLRRAACKHQKEITVVARGP
Retrocopy DLRVCDESSCKYGGVCKEDGDGLKCACQFQCHTNYIPVCGSNGDTYQNECFLRRAACKHQKEITVVARGP

Parental  CYSDNGSGSGEGAEEEGSGAEVHRKHSKCGPCKYKAECDEDAENVGCVCNIDCSGYSFNPVCASDGSSYN
          CYSDNGSGSGEGAEEEGSGAEVHRKHSKCGPCKYKAECDEDAENVGCVCNIDCSGYSFNPVCASDGSSYN
Retrocopy CYSDNGSGSGEGAEEEGSGAEVHRKHSKCGPCKYKAECDEDAENVGCVCNIDCSGYSFNPVCASDGSSYN

Parental  NPCFVREASCIKQEQIDIRHLGHCTDTDDTSLLGKKDDGLQYRPDVKDASDQREDVYIGNHMPCPENLNG
          NPCFVREASCIKQEQIDIRHLGHCTDTDDTSLLGKKDDGLQYRPDVKDASDQREDVYIGNHMPCPENLNG
Retrocopy NPCFVREASCIKQEQIDIRHLGHCTDTDDTSLLGKKDDGLQYRPDVKDASDQREDVYIGNHMPCPENLNG

Parental  YCIHGKCEFIYSTQKASCR
          YCIHGKCEFIYSTQKASCR
Retrocopy YCIHGKCEFIYSTQKASCR

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	0.07 RPM	0.14 RPM
ERP005899_muscle	0.74 RPM	3.70 RPM
SRP017611_brain	2.79 RPM	10.23 RPM
SRP017611_kidney	0.59 RPM	1.90 RPM
SRP017611_liver	0.00 RPM	0.08 RPM
SRP030211_testis	1.90 RPM	16.00 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1811 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1811 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021991	1 retrocopy	retro_btau_1811 ,
Choloepus hoffmanni	ENSCHOG00000010971	3 retrocopies	retro_chof_1673, retro_chof_449, retro_chof_881,
Tursiops truncatus	ENSTTRG00000014374	1 retrocopy	retro_ttru_278,