RetrogeneDB ID: retro_cfam_652

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:10544327..10544986(+)
• Located in intron of: ENSCAFG00000003903

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF7
• Ensembl ID: ENSCAFG00000029620
• Aliases: None
• Description: serine/arginine-rich splicing factor 7 [Source:HGNC Symbol;Acc:10789]

Sequence

>retro_cfam_652
ATATCACCTTACAGGTGGTATGGAGGAGAAAACCAAGGTATATGTTGGTAATCTGGGAACTGGTGTCAGCAGAAGAGAGT
TAAAAAGGGCTTTCAGTTATTACGGTCCTTTAAGAACTGTGTGGATTGTGAAAAATCCTCCAGGATTTCCCTTTGTGGAA
TTTGAAGATCCAACACATGCAGAAGATGCAGTGCAAGATCTGGATGGGAAGGTGATTTGTGGTTCCAGAATGAGAGTTGA
ATTACCAACAGGCATGCTTTGGAGATCTGATTTTGAAAATAGACCACTTGCCCAACATTCATTTGGTCCCAGTGATAAGT
GTGGCAAAAAAGGACATCATGCTTATGATTGTCATCATTACAGTCAGCAGAGGGGAAGCAGGTTACAGTCTAGATCATAT
TTAAGATCCAGAGGTAGGCGATACTCACACTCATGTAGCAGGAGCAGGGAGAAAGGTCAAGATCAGGATCTCCTCGACCA
ACAAAATCAGCTTAACACAGAGGATCTAGGGCTGGTTCTATAAAAGGATAAAGATCTCCATCAAGGTCAGGGTCAAGATC
CAGGTCTGTTTCACTGCCAAGAATCAGTCAAAGTCCAGATCTCTATCTACAAAAAGAAATCATTCCCCATCAGGAAGTCC
ATAAAGAAGTGCAAGTCCT

Alignment

ORF - retro_cfam_652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.45 %
• Parental protein coverage: 94.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSRYGRYGGE-TKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDG
          .S.Y..YGGE.TKVYVGNLGTG....EL.RAFSYYGPLRTVWI..NPPGF.FVEFEDP..AEDAV..LDG
Retrocopy ISPYRWYGGE>TKVYVGNLGTGVSRRELKRAFSYYGPLRTVWIVKNPPGFPFVEFEDPTHAEDAVQDLDG

Parental  KVICGSRVRVELSTGMPRRSRFD-RPPARRPFDPNDRCYECGEKGHYAYDCHRYSRRRRSRSRSRSHSRS
          KVICGSR.RVEL.TGM..RS.F..RP.A...F.P.D.C...G.KGH.AYDCH.YS..R.SR..SRS..RS
Retrocopy KVICGSRMRVELPTGMLWRSDFENRPLAQHSFGPSDKC---GKKGHHAYDCHHYSQQRGSRLQSRSYLRS

Parental  RGRRYSRSRSRSR-GRRSRSASPRRSRSVSLRRSRSASLRRSRSGSIKGSRYFQSRSRS-RSRSRSLSRP
          RGRRYS.S.SRSR.G.RSRS.SPR...S...R.SR..S....RS.S..GSR...SRS.S......S.SR.
Retrocopy RGRRYSHSCSRSR<GERSRSGSPRPTKSA*HRGSRAGSIKG*RSPSRSGSR---SRSVS<TAKNQSKSRS

Parental  RSS-RSKSRSPSPKRSRSP
          .S..R..S.S.SP.RS.SP
Retrocopy LSTKRNHSPSGSP*RSASP

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	49.98 RPM
SRP017611_brain	0.00 RPM	27.71 RPM
SRP017611_kidney	0.00 RPM	34.87 RPM
SRP017611_liver	0.00 RPM	17.98 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_652 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_652 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_652 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015988	1 retrocopy	retro_amel_1025,
Canis familiaris	ENSCAFG00000009289	1 retrocopy	retro_cfam_392,
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	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,