RetrogeneDB ID: retro_btau_473

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:56443649..56444759(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000020684
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_473
ATGGCATATCACAGCTTCCTGGTGGAGTCCATCAGCTGTCACGCCTGGAACAAGGACCGCACCCAGATCGCCATCTGCCC
CAACAACCACGAGGTGCACATCTATGAGAAGAGCGGGAACAAGTGGGTCCAGGAGCACGAACTCAAGGAGCACAACTGGC
AGGTGACAGGCACTGACTGGGCCCCAGAGACTAACCGCATCGTGACTTGCGGCACAGACCGCAACGCCAACGTGTGGACG
CTGAAGGGCCGCACGTGGAAGCCCACGCTTGTCATCCTGCGCATCAACCGCGCCGCTCGCTGTGTGCGCTGGGCCCCCAG
TGAGAAAAAGTTCGCTGTGGGCAGTGGCTCCCCTGTCATCTCCATCTGCTATTTTGAGCAGGAAAATGACTGGTGGGTGT
GCAAGCACATCAAGAAGCCCATCCGCTCCACCGTCCTCAGCCTGGACTGGCACCCCAACAACGTGCTCCTGGCCGCCGGC
TCCTGTGACTTCAAATGCCGGATCTTCTCAGCCTACATCAAGGAGGTGGAGGAGCGGCCAGCACCCACCCCGTGGGGCTC
CAAGATGCCGTTCGGGGAGCTGATGTTCGAATCCAGCAGTAGCTGCGGCTGGGTGCACGGCGTCTGCTTCTCAGCCAACG
GCAGTCGTGTGGCCTGGGTCAGCCATGACAGCACCCTGTGCCTGGTCGATGCTGACAAGAAGATGGCCTTCGAGACTCTG
GCCTCTGAAACGCTGCTGCTGCTGGCCGTCACCTTCATCACGGAGAACAGTCTGGTGGCAGCGGGCCACGACTGCTTCCT
GGTGCTCTTCACCTACGACAGCGCCACGGGGAAGCTGAGCTTCGGTGGGCGGCTGCCCAAGCAGAGATCTCAGCACGGCC
TCACGTCCCGCGAGCGCTTCCAGAACCTCGACAAGAAGGCGAGCTCTGAGGGCAGCGCGGCGGCGGGCGCCGGCCTGGAC
TCGCTGCACAAGAACAGCATCAGCCAGACCTCGGTGCTGAGTGGAGGAAAGGCCAAGTGCTCGCAGTTTTGCACCACCGG
CATGGACGGCGGCATGAGCATCTGGGACGTGAAGAGCCTGGAGTCTGCCCTGAAGGACCTCAAGATCGTA

Alignment

ORF - retro_btau_473 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.01 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGIDWAPDSNRIVTC
          MAYHSFLVE.ISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQ.HELKEHN.QVTG.DWAP..NRIVTC
Retrocopy MAYHSFLVESISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQEHELKEHNWQVTGTDWAPETNRIVTC

Parental  GTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNEKKFAVGSGSRVISICYFEQENDWWVCKHIKKP
          GTDRNA.VWTLKGRTWKPTLVILRINRAARCVRWAP.EKKFAVGSGS.VISICYFEQENDWWVCKHIKKP
Retrocopy GTDRNANVWTLKGRTWKPTLVILRINRAARCVRWAPSEKKFAVGSGSPVISICYFEQENDWWVCKHIKKP

Parental  IRSTVLSLDWHPNSVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCF
          IRSTVLSLDWHPN.VLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCF
Retrocopy IRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCF

Parental  SANGSRVAWVSHDSTVCLADADKKMAVATLASETLPLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLS
          SANGSRVAWVSHDST.CL.DADKKMA..TLASETL.LLAVTFITE.SLVAAGHDCF.VLFTYDSA.GKLS
Retrocopy SANGSRVAWVSHDSTLCLVDADKKMAFETLASETLLLLAVTFITENSLVAAGHDCFLVLFTYDSATGKLS

Parental  FGGRLDVPKQSSQRGLTARERFQNLDKKASSEGSAAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGM
          FGGRL..PKQ.SQ.GLT.RERFQNLDKKASSEGSAAAGAGLDSLHKNS.SQ.SVLSGGKAKCSQFCTTGM
Retrocopy FGGRL--PKQRSQHGLTSRERFQNLDKKASSEGSAAAGAGLDSLHKNSISQTSVLSGGKAKCSQFCTTGM

Parental  DGGMSIWDVRSLESALKDLKIV
          DGGMSIWDV.SLESALKDLKIV
Retrocopy DGGMSIWDVKSLESALKDLKIV

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	0.00 RPM	191.04 RPM
SRP017611_brain	0.09 RPM	15.71 RPM
SRP017611_kidney	0.24 RPM	59.75 RPM
SRP017611_liver	0.00 RPM	37.23 RPM
SRP030211_testis	0.08 RPM	20.83 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_473 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_473 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,