RetrogeneDB ID: retro_btau_1547

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:92298474..92299040(+)
• Located in intron of: ENSBTAG00000014373

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1B
• Ensembl ID: ENSBTAG00000046248
• Aliases: None
• Description: Actin-related protein 2/3 complex subunit 1B [Source:UniProtKB/Swiss-Prot;Acc:Q58CQ2]

Sequence

>retro_btau_1547
AGTGAGAACAGATTCGCCATGGGCAGCAGGGCATGACTCATCTTTGTTTGGTACTTCGAGTCTGAAAATGACTGGTATGT
GAGCAAGCACGTTAAAAAGCCCACCCGCTCCACGGTCCTCAGCTTGGACTGGCATCCCAACAACGTTTTGCTGGCAGTGG
GATCCTGTGACTTCAATGAAGAGTGCTTTCTACCTACATTAAAGAAGTGGATGAGAAGCCAGCCAGTACGCCCTGGGGTG
GCAAAATGCCTTTCAGTCAGCTGATGTCAGAGTATGGAGGCAGGGCACACGGGCTCAGCTTCTCGGCCAGCGGCAGCCGC
CTGGCTTGGGTCAGCCACAACAGCACTGTGTCCACTGCCAACGCCTCAAAAAGCATGCAAGTCTCAACCCTAAAGGTGGA
GTTCCTGCCCCTCCTGAGTGTGTCGTTTGTCTCAGAGAATAGCATCGTGGCTGCTGGCCATGACTGCTGCCCCATGCTCT
TTAACAAGAACAATCACAGCTGCTTGACCTTCGTCACCAAGCTGGACATCCCCAAACAGAGCATCCAACACAATATGGAC
AAGCGG

Alignment

ORF - retro_btau_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.76 %
• Parental protein coverage: 51.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NEKKFAVGSGSRVISICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNSVLLAAGSCDF-KCRIFSAYIKE
          .E..FA.GS....I...YFE.ENDW.V.KH.KKP.RSTVLSLDWHPN.VLLA.GSCDF...R..S.YIKE
Retrocopy SENRFAMGSRA*LIFVWYFESENDWYVSKHVKKPTRSTVLSLDWHPNNVLLAVGSCDF<Q*RVLSTYIKE

Parental  VEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATLASETL
          V.E.PA.TPWG.KMPF..LM.E.....G..HG..FSA.GSR.AWVSH.STV..A.A.K.M.V.TL..E.L
Retrocopy VDEKPASTPWGGKMPFSQLMSEYG---GRAHGLSFSASGSRLAWVSHNSTVSTANASKSMQVSTLKVEFL

Parental  PLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLSFGGRLDVPKQSSQRGLTAR
          PLL.V.F..E.S.VAAGHDC.P.LF........L.F...LD.PKQS.Q.....R
Retrocopy PLLSVSFVSENSIVAAGHDCCPMLFNKNNHS-CLTFVTKLDIPKQSIQHNMDKR

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	11.46 RPM
ERP005899_muscle	0.05 RPM	191.04 RPM
SRP017611_brain	0.00 RPM	15.71 RPM
SRP017611_kidney	0.00 RPM	59.75 RPM
SRP017611_liver	0.00 RPM	37.23 RPM
SRP030211_testis	0.02 RPM	20.83 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1547 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1547 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004242	1 retrocopy	retro_btau_1486,
Bos taurus	ENSBTAG00000046248	2 retrocopies	retro_btau_1547 , retro_btau_473,
Canis familiaris	ENSCAFG00000015081	1 retrocopy	retro_cfam_1568,
Callithrix jacchus	ENSCJAG00000015849	1 retrocopy	retro_cjac_2365,
Echinops telfairi	ENSETEG00000009924	2 retrocopies	retro_etel_1076, retro_etel_1275,
Gorilla gorilla	ENSGGOG00000013186	2 retrocopies	retro_ggor_1337, retro_ggor_1455,
Microcebus murinus	ENSMICG00000017424	1 retrocopy	retro_mmur_602,
Myotis lucifugus	ENSMLUG00000010933	1 retrocopy	retro_mluc_974,
Mustela putorius furo	ENSMPUG00000016522	1 retrocopy	retro_mputfur_1578,
Mus musculus	ENSMUSG00000029622	2 retrocopies	retro_mmus_1340, retro_mmus_3623,
Otolemur garnettii	ENSOGAG00000010872	2 retrocopies	retro_ogar_2380, retro_ogar_3087,
Rattus norvegicus	ENSRNOG00000000991	2 retrocopies	retro_rnor_1105, retro_rnor_967,
Sus scrofa	ENSSSCG00000007625	1 retrocopy	retro_sscr_374,