RetrogeneDB ID: retro_sscr_1038

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:120033583..120034061(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF3
• Ensembl ID: ENSSSCG00000001564
• Aliases: None
• Description: serine/arginine-rich splicing factor 3 [Source:HGNC Symbol;Acc:10785]

Sequence

>retro_sscr_1038
GACTCCTGTCCTTTGGACTGTAAAGGTTATGTAGGTAATCTTGGAAACAGTGGTAACATGATTGAATTGGAATGAGCTTT
TGGCTATTATGGACCACTCCAAAGTGTGTGAGTTGCTAGAAACCCTCCTGGCTTTGCTTTTGTTGAATCTGAAGATTCCC
AAAATGCAGCTGATGCCATCTGAGGGCTAAATGGAAGAACACTGTGTAGCTGCCAAGTAAGAGTAGAACTGTCTGATGGT
GAAAAGAAAAGTAGAAATCGTGGCACACCTCCTTTTTGAGGTTGTCGCCCTCGAGATAATCATCGGAGATGGCGTCTTCC
ACTTCGCCACAGATCTCTGAGACAGAGAAGCTTCTCTGGCAGCTGGATCAGGTCCCTTTCTAGAGACAGGAGAGAGATCA
CTTTCTCAGAGGAGAAATCACAAGCCATCTTGATATTTCTCTAGGTCTCATAGCCGATCTAGGTCAAGTGAAAGGAAA

Alignment

ORF - retro_sscr_1038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 98.17 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGGTLCG
          DSCPLDCK.YVGNLGN.GN..ELE.AFGYYGPL.SV.VARNPPGFAFVE.ED...AADA...L.G.TLC.
Retrocopy DSCPLDCKGYVGNLGNSGNMIELE*AFGYYGPLQSV*VARNPPGFAFVESEDSQNAADAI*GLNGRTLCS

Parental  CRVRVELSNGEKRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSRDRR-RERSLSRE
          C.VRVELS.GEK.SRNRG.PP..G.RPRD..RR...P.R.RS.R.RSFS.S..RSLSRDRR.R..S..R.
Retrocopy CQVRVELSDGEKKSRNRGTPPF*GCRPRDNHRRWRLPLRHRSLRQRSFSGSWIRSLSRDRR>RSLSQRRN

Parental  RNHKPSRSFSRSRSRSRSNERK
          .......S.S.SR..SRS.ERK
Retrocopy HKPS*YFSRSHSR--SRSSERK

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	10.62 RPM
SRP014902_testis	0.00 RPM	14.99 RPM
SRP018288_heart	0.03 RPM	16.66 RPM
SRP018288_kidney	0.00 RPM	15.96 RPM
SRP018288_liver	0.00 RPM	8.00 RPM
SRP018288_lung	0.00 RPM	30.34 RPM
SRP018856_adipose	0.00 RPM	22.15 RPM
SRP035408_brain	0.00 RPM	5.30 RPM
SRP035408_liver	0.00 RPM	5.37 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1038 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1038 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 108 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000040006	5 retrocopies	retro_btau_1176, retro_btau_1442, retro_btau_1445, retro_btau_1665, retro_btau_1813,
Callithrix jacchus	ENSCJAG00000016062	5 retrocopies	retro_cjac_1035, retro_cjac_1969, retro_cjac_2006, retro_cjac_620, retro_cjac_746,
Dasypus novemcinctus	ENSDNOG00000000421	9 retrocopies	retro_dnov_1326, retro_dnov_1513, retro_dnov_1702, retro_dnov_1951, retro_dnov_2153, retro_dnov_2328, retro_dnov_2491, retro_dnov_569, retro_dnov_784,
Equus caballus	ENSECAG00000018741	2 retrocopies	retro_ecab_178, retro_ecab_961,
Echinops telfairi	ENSETEG00000010117	2 retrocopies	retro_etel_2064, retro_etel_445,
Homo sapiens	ENSG00000112081	4 retrocopies	retro_hsap_2140, retro_hsap_2299, retro_hsap_2304, retro_hsap_757,
Gorilla gorilla	ENSGGOG00000017186	5 retrocopies	retro_ggor_1654, retro_ggor_1706, retro_ggor_2030, retro_ggor_2746, retro_ggor_630,
Loxodonta africana	ENSLAFG00000018193	2 retrocopies	retro_lafr_1219, retro_lafr_80,
Microcebus murinus	ENSMICG00000004674	5 retrocopies	retro_mmur_1090, retro_mmur_160, retro_mmur_287, retro_mmur_710, retro_mmur_916,
Myotis lucifugus	ENSMLUG00000010671	6 retrocopies	retro_mluc_1205, retro_mluc_1312, retro_mluc_1554, retro_mluc_2283, retro_mluc_278, retro_mluc_51,
Macaca mulatta	ENSMMUG00000014306	4 retrocopies	retro_mmul_1007, retro_mmul_1042, retro_mmul_1642, retro_mmul_2359,
Mustela putorius furo	ENSMPUG00000014215	1 retrocopy	retro_mputfur_613,
Mus musculus	ENSMUSG00000071172	9 retrocopies	retro_mmus_100, retro_mmus_1347, retro_mmus_1749, retro_mmus_2294, retro_mmus_2337, retro_mmus_2433, retro_mmus_2654, retro_mmus_2933, retro_mmus_3629,
Oryctolagus cuniculus	ENSOCUG00000006684	3 retrocopies	retro_ocun_415, retro_ocun_772, retro_ocun_970,
Otolemur garnettii	ENSOGAG00000000502	6 retrocopies	retro_ogar_1850, retro_ogar_1959, retro_ogar_2131, retro_ogar_2783, retro_ogar_597, retro_ogar_803,
Ochotona princeps	ENSOPRG00000006006	3 retrocopies	retro_opri_1037, retro_opri_158, retro_opri_545,
Pan troglodytes	ENSPTRG00000018106	4 retrocopies	retro_ptro_1566, retro_ptro_1628, retro_ptro_2776, retro_ptro_533,
Rattus norvegicus	ENSRNOG00000000520	11 retrocopies	retro_rnor_1010, retro_rnor_1283, retro_rnor_1321, retro_rnor_1339, retro_rnor_1647, retro_rnor_1697, retro_rnor_1889, retro_rnor_2424, retro_rnor_634, retro_rnor_728, retro_rnor_790,
Sus scrofa	ENSSSCG00000001564	1 retrocopy	retro_sscr_1038 ,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745,
Ictidomys tridecemlineatus	ENSSTOG00000014280	5 retrocopies	retro_itri_123, retro_itri_502, retro_itri_664, retro_itri_857, retro_itri_901,
Tarsius syrichta	ENSTSYG00000013498	3 retrocopies	retro_tsyr_1867, retro_tsyr_2163, retro_tsyr_848,
Tursiops truncatus	ENSTTRG00000013447	11 retrocopies	retro_ttru_105, retro_ttru_1195, retro_ttru_1577, retro_ttru_1628, retro_ttru_1639, retro_ttru_1653, retro_ttru_1677, retro_ttru_1731, retro_ttru_1892, retro_ttru_610, retro_ttru_916,
Vicugna pacos	ENSVPAG00000005481	1 retrocopy	retro_vpac_541,