RetrogeneDB ID: retro_rnor_478

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:132727238..132727922(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Srsf7
• Ensembl ID: ENSRNOG00000027360
• Aliases: Srsf7, Sfrs7
• Description: splicing factor, arginine/serine-rich 7 [Source:RefSeq peptide;Acc:NP_001034124]

Sequence

>retro_rnor_478
CAGTATGGAGGAGAAAGCAAGGGATATGTTGGTAACCTGGGAACTGGTGTGGGTAAAGGAGAGTTAGAAAGAGCATTCAG
TTACTATGGACCCTTAAGAACTGTATGGATTGCCAGAAATCCTCCAGGATTTGCCTTTGTGGATTTGAAGACCCTAGAGA
TGCAGAGGATGCGGTTGGAGGATTGGGTGGGAAAGTGATTTGTGGTTCTCGAGTGAGGGTTGAATTATCAACAGGCATGC
CTCGGAGATCTCGTTTTGATAGGCCACCTGCCTGTCATCCCTTTGATCCTAATGATAGATGCTATGAGTGTGGTGAACAG
GGACATTATGCTTATGACTATCATCGCTGTAGCCGACGAAGAAGCAGGTCACGATCTAGATCACATTCCGGATCCAAGGG
AAGGCGATACTCTTACTCACGCAGCAGGAGCTGCGGAAGGAGGTCAAGATCAACATCTCCTCTATGATCAAGGTCTGTGT
CTCTTCCTAGTTCAAGATCAACTTCACTCAGAAGATCTAAGTCTGTTTCTATAATAGGATCGAGATCCCACAAGGTCGAG
ATCAAGATCTAGGTCTATTTCATGACCAAGAAGCTGCCAATCAAAATCCAGATCTCCATCTCCTAGAAGAAGTCATTCCC
CATCAGGAAGTCCACATAGGAGTGCAAGTCCAGAAAGAATGGAC

Alignment

ORF - retro_rnor_478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.4 %
• Parental protein coverage: 97.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RYGGETKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVE-FEDPRDAEDAVRGLDGKVICG
          .YGGE.K.YVGNLGTG.GKGELERAFSYYGPLRTVWIARNPPGFAFV..FEDPRDAEDAV.GL.GKVICG
Retrocopy QYGGESKGYVGNLGTGVGKGELERAFSYYGPLRTVWIARNPPGFAFVD<FEDPRDAEDAVGGLGGKVICG

Parental  SRVRVELSTGMPRRSRFDRPPARRPFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRSRGRRYS
          SRVRVELSTGMPRRSRFDRPPA..PFDPNDRCYECGE.GHYAYD.HR.S.RRRSRSRSRSHS.S.GRRYS
Retrocopy SRVRVELSTGMPRRSRFDRPPACHPFDPNDRCYECGEQGHYAYDYHRCS-RRRSRSRSRSHSGSKGRRYS

Parental  RSRSRSRGRRSRSASPRRSRSVSLRRSRSASLRRSRSGSIIGSRYF-QSRSRSRSRSRSISRPRSSRSKS
          .SRSRS.GRRSRS.SP..SRSVSL..SRS.SLRRS.S.SIIGSR....SRSRSRS....IS.PRS..SKS
Retrocopy YSRSRSCGRRSRSTSPL*SRSVSLPSSRSTSLRRSKSVSIIGSRSH>RSRSRSRS----IS*PRSCQSKS

Parental  RSPSPKRSRSPSGSPHRSASPERMD
          RSPSP.RS.SPSGSPHRSASPERMD
Retrocopy RSPSPRRSHSPSGSPHRSASPERMD

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
SRP017611_brain	0.14 RPM	38.03 RPM
SRP017611_kidney	0.28 RPM	33.57 RPM
SRP017611_liver	0.27 RPM	25.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_478 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_478 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 36 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	ENSMUSG00000024097	1 retrocopy	retro_mmus_3288,
Otolemur garnettii	ENSOGAG00000010169	2 retrocopies	retro_ogar_3467, retro_ogar_3481,
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,
Rattus norvegicus	ENSRNOG00000005513	1 retrocopy	retro_rnor_2900,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752,
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,