RetrogeneDB ID: retro_mmus_3288

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:71908845..71909550(+)
• Located in intron of: ENSMUSG00000032228

Retrocopy information

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

Parental gene information

• Parental gene symbol: Srsf7
• Ensembl ID: ENSMUSG00000024097
• Aliases: Srsf7, 35kDa, 9430065L19Rik, 9G8, NX-96, Sfrs7
• Description: serine/arginine-rich splicing factor 7 [Source:MGI Symbol;Acc:MGI:1926232]

Sequence

>retro_mmus_3288
TCATGTTACAGGCGGCATGGAGGAGAAACCAAGCTATATGTTGGTAACCTGGGAACTGGTGCTGGTAAAGGAGAGTTAGA
AAGGGCATTCAGTTACTAAGGGCCCTTAGGAACTATATGGATTGCCAGAAATCCTCCAGGATTTGCCTTTGTGGAATTTG
AAGACTTTAGAGATGCAGAGGATGCAGTTCGAGGATTGGATGGGAAAGTGATTTGTGGTTCTGAGTGAGGGTTGAATTAT
CAACAGGCATGCCTCGGAGATCTCTTTTTGATAGGTCACCTGCCCGTCTTCCCTTTGATCCTAATGATAGATGCTATGAG
TGTGGTGAAAAGGGACGTTATGCTTATGACTGTTGTCGCTATAGCTGACGAGGAAGAAGCGGGTCATGATCTAGATCACA
TTCTCGATCCAGGGGAAGGCGATCCTCTTGCTCAAGCAGCCGGAGCCGAGGAAGGAGGTCCAGATCAGCATCTCCTCGAC
ACTCAAGGTCTGTGTCTCTTCGGAGATCGAGATCAGCTTCACTCAGGAGATCTAGGTCTGGTTCTATAATAGGATTGAGT
TATTTCCAATCCTGCTCAAGGTCGAGATCAAGATCCGGGTCTATTTTACGACCAAGAAGCAGCCGATCAAAATCTAGATC
TCTACCTCCTAAAAGATTCCTCATCAGGAAGTCCACACAGAAGTGCAAGTCCAGAAAGAAAGGAC

Alignment

ORF - retro_mmus_3288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.68 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRYGRYGGETKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV
          S.Y.R.GGETK.YVGNLGTGAGKGELERAFSY.GPL.T.WIARNPPGFAFVEFED.RDAEDAVRGLDGKV
Retrocopy SCYRRHGGETKLYVGNLGTGAGKGELERAFSY*GPLGTIWIARNPPGFAFVEFEDFRDAEDAVRGLDGKV

Parental  ICGSR-VRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRSRG
          ICGS..VRVELSTGMPRRS.FDR.PAR.PFDPNDRCYECGEKG.YAYDC.RYS.R.RS.S.SRSHSRSRG
Retrocopy ICGSE<VRVELSTGMPRRSLFDRSPARLPFDPNDRCYECGEKGRYAYDCCRYS*RGRSGS*SRSHSRSRG

Parental  RRYSRSRSRSRGRRSRSASPRRSRSVSLRRSRSASLRRSRSGSIIGSRYFQSRSRSRSRSRSISRPRSSR
          RR.S.S.SRSRGRRSRSASPR.SRSVSLRRSRSASLRRSRSGSIIG..YFQS.SRSRSRS.SI.RPRSSR
Retrocopy RRSSCSSSRSRGRRSRSASPRHSRSVSLRRSRSASLRRSRSGSIIGLSYFQSCSRSRSRSGSILRPRSSR

Parental  SKSRSPSPKRSR-SPSGSPHRSASPERMD
          ..S.S.S....R.S.SGSPHRSASPER.D
Retrocopy --SKSRSLPPKR>SSSGSPHRSASPERKD

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	0.02 RPM	72.45 RPM
SRP007412_cerebellum	0.09 RPM	61.05 RPM
SRP007412_heart	0.03 RPM	31.47 RPM
SRP007412_kidney	0.06 RPM	41.73 RPM
SRP007412_liver	0.00 RPM	22.07 RPM
SRP007412_testis	0.09 RPM	49.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3288 was not detected

EST

No EST(s) were mapped for retro_mmus_3288 retrocopy.

TSS

No TSS is located nearby retro_mmus_3288 retrocopy 5' end.

Lab

retro_mmus_3288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3288 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015988	1 retrocopy	retro_amel_1025,
Canis familiaris	ENSCAFG00000029620	1 retrocopy	retro_cfam_652,
Dasypus novemcinctus	ENSDNOG00000007821	2 retrocopies	retro_dnov_317, retro_dnov_829,
Macropus eugenii	ENSMEUG00000016459	1 retrocopy	retro_meug_1048,
Myotis lucifugus	ENSMLUG00000009536	2 retrocopies	retro_mluc_2005, retro_mluc_972,
Monodelphis domestica	ENSMODG00000008669	1 retrocopy	retro_mdom_289,
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,
Otolemur garnettii	ENSOGAG00000010169	2 retrocopies	retro_ogar_3467, retro_ogar_3481,
Rattus norvegicus	ENSRNOG00000027360	11 retrocopies	retro_rnor_1535, retro_rnor_1977, retro_rnor_1984, retro_rnor_2419, retro_rnor_2420, retro_rnor_2421, retro_rnor_2495, retro_rnor_2501, retro_rnor_2502, retro_rnor_2503, retro_rnor_478,
Sarcophilus harrisii	ENSSHAG00000015970	1 retrocopy	retro_shar_72,