RetrogeneDB ID: retro_sscr_374

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:81047630..81048292(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1B
• Ensembl ID: ENSSSCG00000007625
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1B, 41kDa [Source:HGNC Symbol;Acc:704]

Sequence

>retro_sscr_374
CAGATTGCCCCTAGCCCCAATAATCATGAAGTCCATATAGATAAGAAGAATGGGAGCTAGTGGATAAAAGCTCATTAACT
CAAGGAGCACAACGGACACATTGCAGGTGTTGACTGGGCTTCCAAGAGTGACCGCATCGTCACTTGCGGGGCAGACCGCA
ACACCTATGCCTGGAGTCGGAAAAGATGGTGTCTGGAAGCCAATGCGGGTGATCCTGAGAATTAACCGTGCAGCTACTTT
CGTCAAGTGGTCTCCGCTGGAGAGCAAATTTGCTGTGGGCAGCGGAGCATGACATTTGTTTGTTGCTTGGAGTCTGAAAA
TGGCTGGTGAGTGAGCAAGCACATTAAAAAGCCGATTTGCTCCACAGTCCTCCTCAGCTTGGATTGGCATCCCAACAATG
CCTTGCTGGAGGCAGGATCATGTGATTTCAAATGCAGAGTGTTTCTGGCCTACATTAAAGAAGTGGATGAAAGCCAGCCA
ATACACACTGGGGCAGCAAGATGCCTTTTGGTCAGCTGATGTCAGAGTTTGGTGGCAGTGGCACTGGTGGCTGGGTACAC
AGGGACAGCTTCCCTGCCAGCGGGAGCCGCCTGGCCTGGATCAGCCACGACAGCACTATGCGTGCTGCTCATGCCACAAA
AAGTGTGCAGATCTCAATTCTG

Alignment

ORF - retro_sscr_374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.67 %
• Parental protein coverage: 85.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGIDWAPESNRIVTCGTDRNAYVWTL-KGRTWKPTL
          .IA..PNNHEVHI..K.G..W...H.LKEHNG...G.DWA..S.RIVTCG.DRN.Y.W...K...WKP..
Retrocopy QIAPSPNNHEVHIDKKNGS*WIKAH*LKEHNGHIAGVDWASKSDRIVTCGADRNTYAWSR>KDGVWKPMR

Parental  VILRINRAARCVRWAPQENKFAVGSG-SRVISICYFEQENDWWVCKHIKKPIRSTV-LSLDWHPNNVLLA
          VILRINRAA..V.W.P.E.KFAVGSG.S.....C..E.EN.W.V.KHIKKPI.STV.LSLDWHPNN.LL.
Retrocopy VILRINRAATFVKWSPLESKFAVGSG<SMTFVCC-LESENGW*VSKHIKKPICSTVLLSLDWHPNNALLE

Parental  AGSCDFKCRIFSAYIKEVEE-RPAPTPWGSKMPFGELM--FESSSSCGWVHGVCFSASGSRVAWVSHDST
          AGSCDFKCR.F.AYIKEV.E..PA.T.WGSKMPFG.LM..F..S...GWVH...F.ASGSR.AW.SHDST
Retrocopy AGSCDFKCRVFLAYIKEVDE<KPANTHWGSKMPFGQLMSEFGGSGTGGWVHRDSFPASGSRLAWISHDST

Parental  VCLADADKKMAVATL
          ...A.A.K......L
Retrocopy MRAAHATKSVQISIL

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
SRP014902_placenta	0.00 RPM	205.87 RPM
SRP014902_testis	0.00 RPM	48.09 RPM
SRP018288_heart	0.00 RPM	13.02 RPM
SRP018288_kidney	0.00 RPM	23.74 RPM
SRP018288_liver	0.00 RPM	17.59 RPM
SRP018288_lung	0.00 RPM	145.71 RPM
SRP018856_adipose	0.00 RPM	95.15 RPM
SRP035408_brain	0.00 RPM	2.86 RPM
SRP035408_liver	0.00 RPM	8.16 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_374 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_374 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_374 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	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	ENSSSCG00000007609	1 retrocopy	retro_sscr_387,
Sus scrofa	ENSSSCG00000007625	1 retrocopy	retro_sscr_374 ,