RetrogeneDB ID: retro_mmus_1347

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:59977721..59978211(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000093849
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Srsf3
• Ensembl ID: ENSMUSG00000071172
• Aliases: Srsf3, AL024116, Sfrs3, X16
• Description: serine/arginine-rich splicing factor 3 [Source:MGI Symbol;Acc:MGI:98285]

Sequence

>retro_mmus_1347
ATGCATCGTGATTCCTGTCCCTTGGATTGTAAGGTTTATGTAGGTAATCGTGGAAATAATGGAAACAAGACTGAATTAGA
ACGGGCTTTTGGCTATTATGGACCACTCAGAAATGTGTGGGTTGCTCGAAACCCTCCTGGCTTTGCTTTCGTCGAATTTG
AGGATCCCCGAGACGATGCTGATGCTGTCCGGGAACTAGATGGAAGAGCACTGTGTGGCTGCTGTGTAAGAGTGGAACTG
TCGAATGATGAAAAGAGAAGTCGGAATCGTGGGCCGCCTCCCCCTTGGGGTCGTAGTCTTCGAGATGATGACCGCAGGAG
GAGTCCTCCACCTCGGCGCAGATCCCCAAGAAGGAAAAGCTTTTCCCGAAGCCGGAGCAGGTCACTTTCTAGAGATAGGA
GAAGAGAAAGGTCTTTGCCTCGTGAGAGAAATCACAAGCCGTCTCGATCCTCTCTAGGTCTCGTAGCCATCTAGGTCAAA
TGAAAGGAAA

Alignment

ORF - retro_mmus_1347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT
          MHRDSCPLDCKVYVGN.GNNGNKTELERAFGYYGPLR.VWVARNPPGFAFVEFEDPRD.ADAVRELDGR.
Retrocopy MHRDSCPLDCKVYVGNRGNNGNKTELERAFGYYGPLRNVWVARNPPGFAFVEFEDPRDDADAVRELDGRA

Parental  LCGCRVRVELSNGEKRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSRDRRRERSLS
          LCGC.VRVELSN.EKRSRNRGPPP.WGR..RDD.RRRSPPPRRRSPRR.SFSRSRSRSLSRDRRRERSL.
Retrocopy LCGCCVRVELSNDEKRSRNRGPPPPWGRSLRDDDRRRSPPPRRRSPRRKSFSRSRSRSLSRDRRRERSLP

Parental  RERNHKPSRS-FSRSRSR-SRSNERK
          RERNHKPSRS..SRSRS..SRSNERK
Retrocopy RERNHKPSRS<LSRSRSH<SRSNERK

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
SRP007412_brain	0.00 RPM	70.09 RPM
SRP007412_cerebellum	0.00 RPM	64.83 RPM
SRP007412_heart	0.00 RPM	53.05 RPM
SRP007412_kidney	0.02 RPM	57.23 RPM
SRP007412_liver	0.00 RPM	20.86 RPM
SRP007412_testis	0.09 RPM	39.61 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1347 was not detected

EST

No EST(s) were mapped for retro_mmus_1347 retrocopy.

TSS

No TSS is located nearby retro_mmus_1347 retrocopy 5' end.

Lab

retro_mmus_1347 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1347 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 109 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	ENSMUSG00000021134	1 retrocopy	retro_mmus_2396,
Mus musculus	ENSMUSG00000024097	1 retrocopy	retro_mmus_3288,
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,
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,