RetrogeneDB ID: retro_btau_707

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:59705888..59707070(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.86861
• Ensembl ID: ENSBTAG00000009761
• Aliases: ACTR2, ARP2
• Description: actin-related protein 2 [Source:RefSeq peptide;Acc:NP_001095683]

Sequence

>retro_btau_707
ATGGACAGCCAGGGCAGGAAGGTGGTGGTGTGCGATAACGGCACCAGGTTTGTGAAGTGTGGATATGTAGGCTCTAACTT
TCCAGAACATGTCTTCCCAGCTTTGGTTGGAAGACCTATTATCAGATCGACCACCAAAGTGGGAAACATTGAAATCAAGG
ATCTTATGCTTGATGATGAGGCAAGTGAATTACGCTCGATGTTAGAAGTTAATTACCCTATGGAAAATGGCATAGTACGA
AATTGGGATGACATGAAACACCTATGGGACTACATATTTGGACCAGAGAAACTTAACATAGATACCAGGAATTGTAAAAT
TCTACTCACAGAATCTCCTATGAACCCAGCCAAAAACAGAGAGAAGATTGTAGAGGTAATGTTTGAAACTTACCAGTTTT
CTGGTGTGTATGTAGCCATCCAGGCAGTCCTGACTTTGTGTGCTCAAGGTTTATTAACTGGAGTTGTGGTGGACTCTGGA
GATGGTGTGACTCACATTTGCCCCGTGTATGAAGGCTTTTCTCTCCCTCACCTTACCAGGAGACTGGATATTGCTGGGAG
GTATATTACCAGATATCTTATCAAGTTGCTTCTGTTGCGGGAATATGCCTTCAACCATTCTGCTGATTTTGAAACAGTTC
GCATGATTAAAGAAAAATTGTGTTATGTGGGATATAATATTGAACGAGAGCAGAAACTGGCCTTAGAAACCACAGTATTG
GTTGAATCTTACACACTCCCAGATGGCCGCATTATCAAAGTTGGGGGAGAGAGGTTTGAAGCACCGGAAGCTCTGTTTCA
GCCTCACTTGATCAATGTCGAGGGAGTAGGTGTTGCTGAATTGCTTTTTAACATAATCCAGGTGGCTGACATTGATACCA
GATCTGAGTTCTGTAAGCACATTGTGCTTTCTGGAGGGTCTACTGTGTACCGTGGTCTGCCATCCTGGTTGGAACGAGAG
CTTAAACAGCTTTACTTAGAACGAGTATTGAAGGGTGATGTGGGAAAACTTTCTAAATTCAAGATCCGCATTGAAGACCC
GCCCCGCAGGAAGCACATGGTTTTCCTGGGAGGTGCAGTTCTAGCGGACATCATGAAGGACAAAGACAACTTCTGGATGA
CCCGACAGGAATACCAAGAAAAGGGTGTTCGTGTGCTGGAGAAACTCGGGATGACGGTTCAA

Alignment

ORF - retro_btau_707 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSQGRKVVVCGKNTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDEASELRSMLEV
          MDSQGRKVVVC...T.FVKCGY.GSNFPEH.FPALVGRPIIRSTTKVGNIEIKDLM..DEASELRSMLEV
Retrocopy MDSQGRKVVVCDNGTRFVKCGYVGSNFPEHVFPALVGRPIIRSTTKVGNIEIKDLMLDDEASELRSMLEV

Parental  NYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNREKIVEVMFETYQFSGVYVAI
          NYPMENGIVRNWDDMKHLWDY.FGPEKLNIDTRNCKILLTE.PMNP.KNREKIVEVMFETYQFSGVYVAI
Retrocopy NYPMENGIVRNWDDMKHLWDYIFGPEKLNIDTRNCKILLTESPMNPAKNREKIVEVMFETYQFSGVYVAI

Parental  QAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTRRLDIAGRDITRYLIKLLLLRGYAFNHSADF
          QAVLTL.AQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTRRLDIAGR.ITRYLIKLLLLR.YAFNHSADF
Retrocopy QAVLTLCAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTRRLDIAGRYITRYLIKLLLLREYAFNHSADF

Parental  ETVRMIKEKLCYVGYNIEQEQKLALETTVLVESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAE
          ETVRMIKEKLCYVGYNIE.EQKLALETTVLVESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAE
Retrocopy ETVRMIKEKLCYVGYNIEREQKLALETTVLVESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAE

Parental  LLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRR
          LLFN.IQ.ADIDTRSEF.KHIVLSGGST.Y.GLPS.LERELKQLYLERVLKGDV.KLSKFKIRIEDPPRR
Retrocopy LLFNIIQVADIDTRSEFCKHIVLSGGSTVYRGLPSWLERELKQLYLERVLKGDVGKLSKFKIRIEDPPRR

Parental  KHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR
          KHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGVRVLEKLG.TV.
Retrocopy KHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGVRVLEKLGMTVQ

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	115.43 RPM
ERP005899_muscle	5.44 RPM	192.47 RPM
SRP017611_brain	3.29 RPM	147.32 RPM
SRP017611_kidney	2.49 RPM	134.01 RPM
SRP017611_liver	1.51 RPM	51.80 RPM
SRP030211_testis	0.92 RPM	51.63 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_707 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_707 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_707 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009761	1 retrocopy	retro_btau_707 ,
Callithrix jacchus	ENSCJAG00000006722	1 retrocopy	retro_cjac_429,
Homo sapiens	ENSG00000138071	1 retrocopy	retro_hsap_1978,
Gorilla gorilla	ENSGGOG00000008505	1 retrocopy	retro_ggor_1435,
Monodelphis domestica	ENSMODG00000003364	2 retrocopies	retro_mdom_1082, retro_mdom_754,
Mus musculus	ENSMUSG00000020152	1 retrocopy	retro_mmus_2989,
Pongo abelii	ENSPPYG00000012359	1 retrocopy	retro_pabe_1877,
Pan troglodytes	ENSPTRG00000011990	1 retrocopy	retro_ptro_1320,