RetrogeneDB ID: retro_btau_1823

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:71676361..71677027(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046463
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP6V1C2
• Ensembl ID: ENSBTAG00000001927
• Aliases: None
• Description: V-type proton ATPase subunit C 2 [Source:RefSeq peptide;Acc:NP_001077122]

Sequence

>retro_btau_1823
ATGGTGGTCCCACGGTCAACCAAGTTGGTCGCTGAGGACAAGGAGGGCAGCCTCTTCACCGTGACTCTGTTTTGAAAAGT
GATCGATGATTTCAAAACCAAAGTCAAAGAGAATAATTTCAGTGTACGAGAATTTTACTATGGTGAAAAAGAAATTAAAA
GGGAAAGGGAAGAGATGACCCGATTGCTGTCGGATAAGAAGCAACAATATCAAACTTCCTGTGTTGCTCTTAAAAAGGGA
TCATCCACCTTCCCGGACCACAAGGTTAAGGTAACCCCGCTAGGGAACCCTGATAGGCCCTCTGCGGGGCAGAGTGGCAG
AGAGAGAGAGAATGAGGGCGAGGGTGAGGGCCCAGTGCTGTGATGGCTCAAGGTCCACTTCAGTGAAGCCTTTGTTGCCT
GGATCCACATCAAGGCACTGAGAGTGTTTGTGAAGTCTGTGCTCAGGTATGGACTGCCAGTGAACTTCCAGGCGGTTCTC
CTCCAGCCTCATAAGAAGTCATGCACCAAACGTTTACGACAGGTTCTGAACTCCATCGTCAGGCATCTGGATGAAATTGC
AGCTGCAAGTATATTGGATGCATCCGTGGAGATCCCTGGACTCCAACTCCACAACCAAGACTAATTTCCTTATGTCTACT
TCCACATCGACCTTAGTCTTCTCGAC

Alignment

ORF - retro_btau_1823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.34 %
• Parental protein coverage: 51.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVVPRSTKLIAEDKEGGLFTVTLFRKVIDDFKTKAKENKFTVREFYYDEKEIKREREEMTRLLSDKKQQY
          MVVPRSTKL.AEDKEG.LFTVTLF.KVIDDFKTK.KEN.F.VREFYY.EKEIKREREEMTRLLSDKKQQY
Retrocopy MVVPRSTKLVAEDKEGSLFTVTLF*KVIDDFKTKVKENNFSVREFYYGEKEIKREREEMTRLLSDKKQQY

Parental  QTSCVALKKGSSTFPDHKVKVTPLGNPDRPAAGQSDRERENEGEGEGPLLRWLKVHFSEAFVAWIHIKAL
          QTSCVALKKGSSTFPDHKVKVTPLGNPDRP.AGQS.RERENEGEGEGP.L.WLKVHFSEAFVAWIHIKAL
Retrocopy QTSCVALKKGSSTFPDHKVKVTPLGNPDRPSAGQSGRERENEGEGEGPVL*WLKVHFSEAFVAWIHIKAL

Parental  RVFVESVLRYGLPVNFQAVLLQPHKKSCTKRLRQVLNSVFRHLDEVAAASILDASVEIPGLQLSNQDYFP
          RVFV.SVLRYGLPVNFQAVLLQPHKKSCTKRLRQVLNS..RHLDE.AAASILDASVEIPGLQL.NQD.FP
Retrocopy RVFVKSVLRYGLPVNFQAVLLQPHKKSCTKRLRQVLNSIVRHLDEIAAASILDASVEIPGLQLHNQD*FP

Parental  YVYFHIDLSLLD
          YVYFHIDLSLLD
Retrocopy YVYFHIDLSLLD

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	1.23 RPM
ERP005899_muscle	0.00 RPM	1.48 RPM
SRP017611_brain	0.00 RPM	1.10 RPM
SRP017611_kidney	0.00 RPM	25.72 RPM
SRP017611_liver	0.23 RPM	29.52 RPM
SRP030211_testis	0.08 RPM	5.10 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1823 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1823 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1823 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001927	1 retrocopy	retro_btau_1823 ,
Callithrix jacchus	ENSCJAG00000006660	2 retrocopies	retro_cjac_1089, retro_cjac_3461,
Monodelphis domestica	ENSMODG00000014803	1 retrocopy	retro_mdom_2006,
Otolemur garnettii	ENSOGAG00000009748	1 retrocopy	retro_ogar_403,
Sarcophilus harrisii	ENSSHAG00000009886	1 retrocopy	retro_shar_33,