RetrogeneDB ID: retro_cfam_392

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:49790379..49791059(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF6
• Ensembl ID: ENSCAFG00000009289
• Aliases: None
• Description: serine/arginine-rich splicing factor 6 [Source:HGNC Symbol;Acc:10788]

Sequence

>retro_cfam_392
TCGTTGCAATCTTGTTGGCAAGATTTAAAGGATTTCATGAGACCAGCAGGTGGAGTGACCCATGCCTACGCGCACAAAGA
ACGCTCAAACCAGGGCCTGATTGAATTCCGTTCCCGCTCCGACATGAAGCTGCTTTGGATAAACCGGATGGTATGGAAAT
AAATGGCAGAAATATTAGGCTCATTGAGGATAAACCACAGAAGGAGCCATAAGCGGTCTTACCCTGGAAGCAGATCAAGG
TCACGGTCTAGAAGAAGGTCACGAAGTGGGAGTCATAGAGCAGCCGCAGTAGATCTCCAAGTATCTCAGAAAGTCGCTCC
CGATCCAGGTCTCAGAGCAAAGGTCGATCACGTTCTCGATCAAAAGTCAGGAAATCTAGATCATAAAGCACATCTAAGCC
CAAGTCAGATGGGGGCTCCCGTTGGCTCTCTCGAAGCAGATCTAAGGAGTATGAGCAATCTCGAAGCAGGTCTTGTTCTC
CACCTCGTTCCCCCAAAGAAAATGGAAAAGGTGATATAAAGTCAAAATCTAGATCAAGAAGCCAGTCTCGTTCAAATTCT
CCCCTTCCTGCCCCACCCTCAAAGGCACGTTCTGTGTCCCCTCCACCAAAAAGAGCTTCAAGATCCCGTTCTAGATCTCA
TTTGAAGTCAAGGTCACGGTCCAGATCCAGTTCCAGAGAT

Alignment

ORF - retro_cfam_392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.48 %
• Parental protein coverage: 65.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSRCSWQDLKDFMRQAGEVTYADAHKERTNEGVIEFRSYSDMK-RALDKLDGTEINGRNIRLIEDKP-RT
          S....WQDLKDFMR.AG.VT.A.AHKER.N.G.IEFRS.SDMK..ALDK.DG.EINGRNIRLIEDKP.R.
Retrocopy SLQSCWQDLKDFMRPAGGVTHAYAHKERSNQGLIEFRSRSDMK<AALDKPDGMEINGRNIRLIEDKP>RR

Parental  SHRRSYSGSRSRSRSRRRSRSRSRR-SSRSRSRSISKSRSRSRSRSKGRSRSRSKGRKSRSKSKSKPKSD
          SH.RSY.GSRSRSRSRRRSRS.S.R.SSRSRS.SIS.SRSRSRS.SKGRSRSRSK.RKSRS.S.SKPKSD
Retrocopy SHKRSYPGSRSRSRSRRRSRSGSHR<SSRSRSPSISESRSRSRSQSKGRSRSRSKVRKSRS*STSKPKSD

Parental  RGSRSRSRSRSKEYEKSRSRSRSRSRSPKENGKGDIKSKSRSRSQSRSNSPLPAPPSKARSVSPPPKRAS
          .GSR..SRSRSKEYE.SRSRS.S..RSPKENGKGDIKSKSRSRSQSRSNSPLPAPPSKARSVSPPPKRAS
Retrocopy GGSRWLSRSRSKEYEQSRSRSCSPPRSPKENGKGDIKSKSRSRSQSRSNSPLPAPPSKARSVSPPPKRAS

Parental  RSRSRSRSKSRSRSRSSSRD
          RSRSRS..KSRSRSRSSSRD
Retrocopy RSRSRSHLKSRSRSRSSSRD

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
SRP012049_cerebellum	0.00 RPM	70.94 RPM
SRP017611_brain	0.00 RPM	46.05 RPM
SRP017611_kidney	0.00 RPM	94.10 RPM
SRP017611_liver	0.00 RPM	52.93 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_392 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_392 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002061	1 retrocopy	retro_acar_191,
Canis familiaris	ENSCAFG00000009289	1 retrocopy	retro_cfam_392 ,
Canis familiaris	ENSCAFG00000029620	1 retrocopy	retro_cfam_652,
Gorilla gorilla	ENSGGOG00000009808	1 retrocopy	retro_ggor_2176,
Monodelphis domestica	ENSMODG00000003107	1 retrocopy	retro_mdom_697,
Oryctolagus cuniculus	ENSOCUG00000009785	1 retrocopy	retro_ocun_312,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752,
Tupaia belangeri	ENSTBEG00000013448	1 retrocopy	retro_tbel_383,