RetrogeneDB ID: retro_sscr_554

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:68258723..68259246(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF10
• Ensembl ID: ENSSSCG00000021615
• Aliases: None
• Description: serine/arginine-rich splicing factor 10 [Source:HGNC Symbol;Acc:16713]

Sequence

>retro_sscr_554
CCCTCCAACATGTCTCCGTTCTTAACAAACATGACCAACAATACCACGTCTGAAGATTTGTGACATGAATTTGGTCATCA
TGGTCCTATAGTTGATGTGTATGTTCCACTTGATTTCTATACTCGTTGCCCAAGAGGATTTGCATATGTTCAATTTGAGG
ATGTTCATGATGCTGAAGATGCTTTACATAATTTGGGCAGAAACTGGATTTGTGGACACAAATTGAAATACAGTTTGCAC
AGGGGGATCAGAAGACTCCAAATCAGATGAAAGCAAAGGAAGGGAGAAAGGTGTAACCATGCTATGATGATTATGACAGA
TAAAGGCATTCTAGAAGCCAAAGTTACAAAAGAAGGAGATCAAGAAGTTGGTCCTTTGATTACAACTATAAAAGATCTTA
TAGTCCCAGAAAGAGTAGACCAACTGTAAGACCAGGCGTAGCAGAAGCCATACTGACAATGATAGACCATACTACAGCTG
GAATACCCAGTATAGTTCTGCTTACTACACACCAACAAAGATC

Alignment

ORF - retro_sscr_554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.16 %
• Parental protein coverage: 96.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPNTSLFVRNVAGCFRSEDLRREFGRYGPIVDVYVLLKFWTRWKFLFSYAKFEDVRDAEDALHNLDRKWI
          P.N.S.F..N......SEDL..EFG..GPIVDVYV.L.F.TR....F.Y..FEDV.DAEDALHNL.R.WI
Retrocopy PSNMSPFLTNMTNNTTSEDL*HEFGHHGPIVDVYVPLDFYTRCPRGFAYVQFEDVHDAEDALHNLGRNWI

Parental  CGR-QIEIQFAQGDRKTPNQMKAKEGRNVYSSSRYDDYDRYRRSRSRSYERRRSRSRSFDYNYRRSYSPR
          CG..QIEIQFAQGD.KTPNQMKAKEGR.V.......D..R..R..S.SY.RRRSRS.SFDYNY.RSYSPR
Retrocopy CGH<QIEIQFAQGDQKTPNQMKAKEGRKV*PCYDDYDR*RHSR--SQSYKRRRSRSWSFDYNYKRSYSPR

Parental  NSRPTGRP-RRSRSHSDNDRPNCSWNTQYSSAYYTSRKI
          .SRPT.RP.RRSRSH.DNDRP..SWNTQYSSAYYT..KI
Retrocopy KSRPTVRP<RRSRSHTDNDRPYYSWNTQYSSAYYTPTKI

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	13.27 RPM
SRP014902_testis	0.00 RPM	47.95 RPM
SRP018288_heart	0.00 RPM	44.06 RPM
SRP018288_kidney	0.10 RPM	44.03 RPM
SRP018288_liver	0.00 RPM	30.06 RPM
SRP018288_lung	0.00 RPM	59.67 RPM
SRP018856_adipose	0.00 RPM	22.35 RPM
SRP035408_brain	0.10 RPM	18.52 RPM
SRP035408_liver	0.15 RPM	56.33 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_554 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_554 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004836	1 retrocopy	retro_chof_7,
Callithrix jacchus	ENSCJAG00000020883	9 retrocopies	retro_cjac_1126, retro_cjac_1170, retro_cjac_2176, retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus	ENSCPOG00000024533	1 retrocopy	retro_cpor_1098,
Dasypus novemcinctus	ENSDNOG00000008699	3 retrocopies	retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Erinaceus europaeus	ENSEEUG00000014286	1 retrocopy	retro_eeur_522,
Homo sapiens	ENSG00000188529	5 retrocopies	retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054, retro_hsap_4295,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Mustela putorius furo	ENSMPUG00000015845	1 retrocopy	retro_mputfur_353,
Nomascus leucogenys	ENSNLEG00000013180	3 retrocopies	retro_nleu_1647, retro_nleu_1825, retro_nleu_202,
Oryctolagus cuniculus	ENSOCUG00000029326	1 retrocopy	retro_ocun_717,
Pongo abelii	ENSPPYG00000001726	4 retrocopies	retro_pabe_1115, retro_pabe_1601, retro_pabe_1796, retro_pabe_2529,
Sus scrofa	ENSSSCG00000021615	2 retrocopies	retro_sscr_528, retro_sscr_554 ,
Ictidomys tridecemlineatus	ENSSTOG00000000956	1 retrocopy	retro_itri_1333,
Tursiops truncatus	ENSTTRG00000016150	2 retrocopies	retro_ttru_1098, retro_ttru_695,