RetrogeneDB ID: retro_sscr_883

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:105646336..105646714(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINS2
• Ensembl ID: ENSSSCG00000002663
• Aliases: None
• Description: GINS complex subunit 2 (Psf2 homolog) [Source:HGNC Symbol;Acc:24575]

Sequence

>retro_sscr_883
ATAGACCCGGCAGACATGACGTTTGCGGCCCAGAAGGAGACAGTCACCATTATTCCGAACTTCGTTCTAGGCAAGGTCTA
CCTCCTGAGGGGTACCTGGGGCCCTTCCACCCTTGCTTACCAGTGAAGGAGCCTCTGTGGCTGGAGGTTCACCTGAAACC
AAGACAAGGGAGGCTGCTTCGTCCCAAGCAGAGGGATGTAGAAAAGTTGGAAAGAATAAGGGGTCACGAACACAAATTAG
AGACTTTCCCCCCTCGCCTAAAGCTTTTTCCATGGAACTTACCAACCTCCGTTAAAGTAGACTTCAGCCAACATCCCAAA
AGCAGACGCGATCCAGACCCAGCACAGGGACACGCGGGAGACTTGCAGAGCCAAGCTC

Alignment

ORF - retro_sscr_883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.2 %
• Parental protein coverage: 69.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDAAEVEFLAEKELVTIIPNFSLDKIYLIGGD-LGPFNPGLPVQVPLWLAINLKQRQKCRLLAPEWMDVE
          .D.A...F.A.KE.VTIIPNF.L.K.YL..G..LGPF.P.LPV..PLWL...LK.RQ..RLL.P...DVE
Retrocopy IDPADMTFAAQKETVTIIPNFVLGKVYLLRGT<LGPFHPCLPVKEPLWLEVHLKPRQG-RLLRPKQRDVE

Parental  KLEKMRDHERKEDT-FTPAPNPHYTELTKLL-LNHASDNIPKADEIRTLIKDVWDTRVAKL
          KLE..R.HE.K..T.F.P.P.....ELT.L..L...S.NIPKAD.I.T...D...T..AKL
Retrocopy KLERIRGHEHKLET<FPPSPKAFSMELTNLR<LK*TSANIPKADAIQTQHRDTRETCRAKL

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	2.65 RPM
SRP014902_testis	0.00 RPM	7.07 RPM
SRP018288_heart	0.00 RPM	0.71 RPM
SRP018288_kidney	0.00 RPM	2.46 RPM
SRP018288_liver	0.00 RPM	1.60 RPM
SRP018288_lung	0.00 RPM	3.67 RPM
SRP018856_adipose	0.00 RPM	0.91 RPM
SRP035408_brain	0.00 RPM	2.57 RPM
SRP035408_liver	0.00 RPM	3.55 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_883 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017303	1 retrocopy	retro_cjac_3309,
Dasypus novemcinctus	ENSDNOG00000008760	4 retrocopies	retro_dnov_1034, retro_dnov_166, retro_dnov_2424, retro_dnov_604,
Homo sapiens	ENSG00000131153	1 retrocopy	retro_hsap_2477,
Gallus gallus	ENSGALG00000028131	1 retrocopy	retro_ggal_22,
Gorilla gorilla	ENSGGOG00000009069	2 retrocopies	retro_ggor_1542, retro_ggor_960,
Macropus eugenii	ENSMEUG00000014703	1 retrocopy	retro_meug_1479,
Microcebus murinus	ENSMICG00000016691	1 retrocopy	retro_mmur_342,
Macaca mulatta	ENSMMUG00000020594	1 retrocopy	retro_mmul_596,
Pongo abelii	ENSPPYG00000007616	2 retrocopies	retro_pabe_1826, retro_pabe_896,
Pan troglodytes	ENSPTRG00000008430	1 retrocopy	retro_ptro_1433,
Pteropus vampyrus	ENSPVAG00000004944	1 retrocopy	retro_pvam_762,
Sarcophilus harrisii	ENSSHAG00000015249	1 retrocopy	retro_shar_382,
Sus scrofa	ENSSSCG00000002663	1 retrocopy	retro_sscr_883 ,
Tupaia belangeri	ENSTBEG00000006220	1 retrocopy	retro_tbel_1328,