RetrogeneDB ID: retro_cfam_484

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 12:27446480..27446648(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO2
• Ensembl ID: ENSCAFG00000004724
• Aliases: None
• Description: Canis lupus familiaris SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae) (SUMO2), mRNA. [Source:RefSeq mRNA;Acc:NM_001252289]

Sequence

>retro_cfam_484
CCACTTAGTAAACTAATGAAAGCTGGTTGGGAATAATAGGGTTTGTCAATGAGGGAGATCAGATTCCTATGTGATGGGTA
GCCAATCTATGAAATTGACATGCCTGCACAGCTGGAAATGGAGAATGAAGATGTAGTTGATGTTTTATGGCAGCAGACAG
GAGGTGTC

Alignment

ORF - retro_cfam_484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 58.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGV
          PLSKLMKA..E..GLSMR.IRF..DG.PI.E.D.PAQLEME.ED..DV..QQTGGV
Retrocopy PLSKLMKAGWE**GLSMREIRFLCDG*PIYEIDMPAQLEMENEDVVDVLWQQTGGV

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	104.83 RPM
SRP017611_brain	0.00 RPM	52.95 RPM
SRP017611_kidney	0.00 RPM	81.09 RPM
SRP017611_liver	0.00 RPM	20.45 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_484 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_484 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_484 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004724	1 retrocopy	retro_cfam_484 ,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Homo sapiens	ENSG00000188612	2 retrocopies	retro_hsap_4036, retro_hsap_4095,
Gorilla gorilla	ENSGGOG00000023769	3 retrocopies	retro_ggor_101, retro_ggor_184, retro_ggor_2576,
Loxodonta africana	ENSLAFG00000025811	10 retrocopies	retro_lafr_104, retro_lafr_1222, retro_lafr_1240, retro_lafr_200, retro_lafr_254, retro_lafr_324, retro_lafr_36, retro_lafr_488, retro_lafr_858, retro_lafr_888,
Monodelphis domestica	ENSMODG00000007222	11 retrocopies	retro_mdom_1263, retro_mdom_1472, retro_mdom_1474, retro_mdom_1560, retro_mdom_1598, retro_mdom_1755, retro_mdom_237, retro_mdom_378, retro_mdom_517, retro_mdom_788, retro_mdom_986,
Mus musculus	ENSMUSG00000020738	19 retrocopies	retro_mmus_1498, retro_mmus_1772, retro_mmus_1903, retro_mmus_2050, retro_mmus_2323, retro_mmus_2475, retro_mmus_2492, retro_mmus_2590, retro_mmus_2767, retro_mmus_2917, retro_mmus_2974, retro_mmus_3209, retro_mmus_3414, retro_mmus_3630, retro_mmus_415, retro_mmus_611, retro_mmus_689, retro_mmus_818, retro_mmus_827,
Oryctolagus cuniculus	ENSOCUG00000028195	5 retrocopies	retro_ocun_110, retro_ocun_136, retro_ocun_175, retro_ocun_22, retro_ocun_46,
Pongo abelii	ENSPPYG00000029777	2 retrocopies	retro_pabe_164, retro_pabe_84,