RetrogeneDB ID: retro_cfam_498

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:58838093..58838598(+)
• Located in intron of: ENSCAFG00000003554

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRI
• Ensembl ID: ENSCAFG00000001855
• Aliases: None
• Description: sorcin [Source:HGNC Symbol;Acc:11292]

Sequence

>retro_cfam_498
AGGTATGGAGGGGCTCTGGGAGGGCCTACATTTTCCAGACAAACTCAGGATCTTCTGTATAGTTACTTGCTGCTGGAGCT
GTACAGGATGGGCAAGCAGAAACTGATGAACTGCAGAGATGCCTGACACCTGAAGGATACAAACCTTTTAACCTGGAAAC
TTGTTGGCTTATGATTTCAATGCTGGGTACAGATACGTCAGGCACAATGGATTTCAATGAATTTAAAGAACTCTGGGCTG
TAATGAAGGGTTGGACACAACACTTCATCAGTTTTGACAGTGACTGGAGTGGAACAGTGGATCCTCAAGAACTGCAGAGG
GCCCTGACCACAATGGGATTTTGGTTGAGTTCCCAAGCTGTGAATTCAATTGCAAAATGATACGACACCAATTTCAAGAT
CACTTTCAATGACTACATCACCTGCTGCATCAAAATGCCAGCTCTGACAGCTTTCAAAGATGGGATACTGCTCAACAAGG
TGCTGTGAATTTCCCCTATGATGAT

Alignment

ORF - retro_cfam_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.43 %
• Parental protein coverage: 55.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RYGGAPGGPTFPGQTQDPLYGYF-AAVAGQDGQIDADELQRCLTQSGIAGGYKPFNLETCRLMVSMLDRD
          RYGGA.GGPTF..QTQD.LY.Y..AA.A.QDGQ...DELQRCLT......GYKPFNLETC.LM.SML..D
Retrocopy RYGGALGGPTFSRQTQDLLYSYL<AAGAVQDGQAETDELQRCLTPE----GYKPFNLETCWLMISMLGTD

Parental  MSGTMGFNEFKELWAVLNGWRQHFISFDSDRSGTVDPQELQKALTTMGFRLSPQAVNSIAKRYSTNGKIT
          .SGTM.FNEFKELWAV..GW.QHFISFDSD.SGTVDPQELQ.ALTTMGF.LS.QAVNSIAK.Y.TN.KIT
Retrocopy TSGTMDFNEFKELWAVMKGWTQHFISFDSDWSGTVDPQELQRALTTMGFWLSSQAVNSIAK*YDTNFKIT

Parental  FDDYIACCVKLRALTDSFR-RRDTAQQGVVNFPYDD
          F.DYI.CC.K..ALT..F..R.DTAQQG.VNFPYDD
Retrocopy FNDYITCCIKMPALT-AFK<RWDTAQQGAVNFPYDD

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	47.75 RPM
SRP017611_brain	0.00 RPM	40.01 RPM
SRP017611_kidney	0.00 RPM	55.14 RPM
SRP017611_liver	0.00 RPM	20.38 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_498 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_498 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001855	1 retrocopy	retro_cfam_498 ,
Canis familiaris	ENSCAFG00000011044	2 retrocopies	retro_cfam_1289, retro_cfam_1695,
Cavia porcellus	ENSCPOG00000010096	1 retrocopy	retro_cpor_216,
Latimeria chalumnae	ENSLACG00000000210	1 retrocopy	retro_lcha_89,
Loxodonta africana	ENSLAFG00000027380	2 retrocopies	retro_lafr_1186, retro_lafr_487,
Monodelphis domestica	ENSMODG00000010355	1 retrocopy	retro_mdom_782,
Mustela putorius furo	ENSMPUG00000018313	1 retrocopy	retro_mputfur_1147,
Pteropus vampyrus	ENSPVAG00000007438	2 retrocopies	retro_pvam_1112, retro_pvam_734,
Rattus norvegicus	ENSRNOG00000049780	1 retrocopy	retro_rnor_1237,
Ictidomys tridecemlineatus	ENSSTOG00000004372	1 retrocopy	retro_itri_607,
Tupaia belangeri	ENSTBEG00000004434	1 retrocopy	retro_tbel_4493,
Tarsius syrichta	ENSTSYG00000014640	1 retrocopy	retro_tsyr_1832,
Xenopus tropicalis	ENSXETG00000008793	1 retrocopy	retro_xtro_25,