RetrogeneDB ID: retro_sscr_745

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:144371513..144372110(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF9
• Ensembl ID: ENSSSCG00000009906
• Aliases: None
• Description: serine/arginine-rich splicing factor 9 [Source:HGNC Symbol;Acc:10791]

Sequence

>retro_sscr_745
ACGGACATGCGTGAGAAGGACCTGGAGGACATGATCTACAAGTAGGGCCACATCTGCAAGATTGAGCTCAAGAATCAGCA
TGGCCTCATGCCCTTAGCCTTCGTGCACTTTGAGGACCCCTGAGATGCTGAGGATGCCATTTATGGAAGGAACGGTTATG
ACAATGGCCAATGTCGCCTTCATGTGGAGTTCCCCAGGACTTATGGAGGTCAGGGTGGGTGGCCCTGTAGTGGGAGGAAT
GGGCCTCCTACAAGAAGATCTGATTTCCCAGTTCTTGTTTCAGGACTTCCTCCATCAGGCAGCTGGCAAGACCTGAAAGA
TCACATCCGAGAAGCTGGGGACATCTGCTGCGCGGATGTGCAGAAAGATGGAATGGGAATGGTTGAATATCTCAGAAAAG
AAGACATGGAATATACCCTGTGTAAACTGGATGATGCCAAATTCTGCTCTCATGAGGGTGAAACTTCCTACATCCGAGTT
TATCCAGAGAGAAGCACCAGCTATGGCTACTCATGCTCTCCATCTGGGTCAAGGGGCTGTGATTCTCCATATCAAAGCAG
GGGTTCCCCACACTACTTCTCTCCTTTCAGACCCTAC

Alignment

ORF - retro_sscr_745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.93 %
• Parental protein coverage: 90.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TDVREKDLEDLFYKYGRIREIELKNRHGLVPFAFVRFEDPRDAEDAIYGRNGYDYGQCRLRVEFPRTYGG
          TD.REKDLED..YK.G.I..IELKN.HGL.P.AFV.FEDP.DAEDAIYGRNGYD.GQCRL.VEFPRTYGG
Retrocopy TDMREKDLEDMIYK*GHICKIELKNQHGLMPLAFVHFEDP*DAEDAIYGRNGYDNGQCRLHVEFPRTYGG

Parental  RGGWPRGGRNGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKEDMEYAL
          .GGWP..GRNGPPTRRSDF.VLVSGLPPSGSWQDLKDH.REAGD.C.ADVQKDGMGMVEYLRKEDMEY.L
Retrocopy QGGWPCSGRNGPPTRRSDFPVLVSGLPPSGSWQDLKDHIREAGDICCADVQKDGMGMVEYLRKEDMEYTL

Parental  RKLDDTKFRSHEGETSYIRVYPERSTSYGYSRSRSGSRGRDSPYQSRGSPHYFSPFRPY
          .KLDD.KF.SHEGETSYIRVYPERSTSYGYS.S.SGSRG.DSPYQSRGSPHYFSPFRPY
Retrocopy CKLDDAKFCSHEGETSYIRVYPERSTSYGYSCSPSGSRGCDSPYQSRGSPHYFSPFRPY

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	93.71 RPM
SRP014902_testis	0.00 RPM	86.42 RPM
SRP018288_heart	0.03 RPM	11.24 RPM
SRP018288_kidney	0.00 RPM	58.81 RPM
SRP018288_liver	0.16 RPM	30.86 RPM
SRP018288_lung	0.00 RPM	36.86 RPM
SRP018856_adipose	0.00 RPM	67.66 RPM
SRP035408_brain	0.00 RPM	29.51 RPM
SRP035408_liver	0.00 RPM	39.31 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_745 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_745 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_745 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837,
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555, retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
Otolemur garnettii	ENSOGAG00000003852	1 retrocopy	retro_ogar_2328,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Pongo abelii	ENSPPYG00000005031	1 retrocopy	retro_pabe_119,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598,
Sus scrofa	ENSSSCG00000001564	1 retrocopy	retro_sscr_1038,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745 ,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tarsius syrichta	ENSTSYG00000006848	4 retrocopies	retro_tsyr_1432, retro_tsyr_1648, retro_tsyr_585, retro_tsyr_891,