RetrogeneDB ID: retro_ecab_961

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:74868072..74868545(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF3
• Ensembl ID: ENSECAG00000018741
• Aliases: None
• Description: serine/arginine-rich splicing factor 3 [Source:HGNC Symbol;Acc:10785]

Sequence

>retro_ecab_961
GTGCATCATGATTCCTGTCCATTGGACTGTAAGGTTTATACAGGTAATCTTGGAAACAATGGTAACAAGACTGAATTGGA
ACGAGCTTTTGTTTGTTACGGACAACTCCGAAGTGTGTGGGTTGCTAGAAACCCTCCTGCCTTTGCTTTTGTTGAATTTT
AGGATCCCCTAGACGAGGCTGATGCTGTCTGAGAGCTGGATTAGAGAGCAATATGTGGCTGCCGAGTAAGAGTGGTACTG
TGGAATGATGAAAAAAGTCAAAATCGTAGCCCACCTCCCTCTTGGAGTCACCACCCTCAAGACAGTGGAGGAGTCCTCCA
CCTAGACGCAGATCCCCAAGACAGAGAAGCCTCTCCCGTAGCCGGAACAGGTCCCTTTAGAGAGAGAGGAGGAGAGAGAG
ATCACCGTCCCAGAAGAGAAATCACAAGCCGTCGTTATCCTTCTCTAGGTCTCATAGCTGACCTAGGTCAAAC

Alignment

ORF - retro_ecab_961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.14 %
• Parental protein coverage: 98.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT
          .H.DSCPLDCKVY.GNLGNNGNKTELERAF..YG.LRSVWVARNPP.FAFVEF.DP.D.ADAV.ELD.R.
Retrocopy VHHDSCPLDCKVYTGNLGNNGNKTELERAFVCYGQLRSVWVARNPPAFAFVEF*DPLDEADAV*ELD*RA

Parental  LCGCRVRVELSNGEKRSRNRGPPPSWGRRPRD-DYRRRSPPPRRRSPRRRSFSRSRSRSLSRDRRRERSL
          .CGCRVRV.L.N.EK.S.NR.PPPSW...P.D...R...P..RRRSPR.RS.SRSR.RSL........S.
Retrocopy ICGCRVRVVLWNDEK-SQNRSPPPSWSHHPQD<QWRSPPP--RRRSPRQRSLSRSRNRSLXXXXXXXXSP

Parental  SRERNHKPSRSFSRSRSRSRSN
          S..RNHKPS.SFSRS.S..RSN
Retrocopy SQKRNHKPSLSFSRSHS*PRSN

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
SRP021940_articular_cartilage	0.00 RPM	8.85 RPM
SRP021940_cerebellum	0.00 RPM	14.13 RPM
SRP021940_embryo	0.00 RPM	23.60 RPM
SRP021940_placental_villous	0.00 RPM	12.08 RPM
SRP021940_synovial_membrane	0.00 RPM	12.05 RPM
SRP021940_testis	0.00 RPM	16.31 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_961 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_961 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
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 ,
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,
Myotis lucifugus	ENSMLUG00000010671	6 retrocopies	retro_mluc_1205, retro_mluc_1312, retro_mluc_1554, retro_mluc_2283, retro_mluc_278, retro_mluc_51,
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,
Pan troglodytes	ENSPTRG00000018106	4 retrocopies	retro_ptro_1566, retro_ptro_1628, retro_ptro_2776, retro_ptro_533,
Sus scrofa	ENSSSCG00000001564	1 retrocopy	retro_sscr_1038,
Ictidomys tridecemlineatus	ENSSTOG00000014280	5 retrocopies	retro_itri_123, retro_itri_502, retro_itri_664, retro_itri_857, retro_itri_901,