RetrogeneDB ID: retro_cfam_1340

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:35092130..35092572(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V1
• Ensembl ID: ENSCAFG00000032244
• Aliases: None
• Description: Canis lupus familiaris ubiquitin-conjugating enzyme E2 variant 1 (UBE2V1), mRNA. [Source:RefSeq mRNA;Acc:NM_001205096]

Sequence

>retro_cfam_1340
ATGGCAGCCACCACGGGCTCGGGAGTAAAAGTCCCTCACAATTTTCAATTGTTGGAAGAACTGGAAGAAGGCCAGAAAGG
AGTAGGAGATGGCACAGTTAGCTGGGGTCTAGAAGATGACAAAGACATGACACTTACAAGATAGACCGGGATGATAATTG
GGCCTCCAAGAACAATTTATGAAAACTGAATATACAGCCTTAAAATAGAATGTGGACCTAAATACCCAGAAACACCCCCC
CTTTGTAAGATTTGTAACAAAAATTAATATGAATGGAGTTAATAGTTCTAACAGAGTGGTGGATCCAAGGGCCATATCAG
TGCTAGCAAAATGGCAGAATTCATATAGCTTCAAAGTTGTGCTGAAAGAGCTCCTGTGCCTAATGATGTCTAAAGAAAAC
ATGAAACTCCTTCAGCCACCCAAAGGACAGTGTTACAGCAAT

Alignment

ORF - retro_cfam_1340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAATTGSGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTIYENRIYSLKIE
          MAATTGSGVKVP.NF.LLEELEEGQKGVGDGTVSWGLEDD.DMTLTR.TGMIIGPPRTIYEN.IYSLKIE
Retrocopy MAATTGSGVKVPHNFQLLEELEEGQKGVGDGTVSWGLEDDKDMTLTR*TGMIIGPPRTIYEN*IYSLKIE

Parental  CGPKYPEA-PPFVRFVTKINMNGVNSSNGVVDPRAISVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQP
          CGPKYPE..PPFVRFVTKINMNGVNSSN.VVDPRAISVLAKWQNSYS.KVVL.EL..LMMSKENMKL.QP
Retrocopy CGPKYPET>PPFVRFVTKINMNGVNSSNRVVDPRAISVLAKWQNSYSFKVVLKELLCLMMSKENMKLLQP

Parental  PEGQCYSN
          P.GQCYSN
Retrocopy PKGQCYSN

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	0.04 RPM	68.00 RPM
SRP017611_brain	0.00 RPM	58.12 RPM
SRP017611_kidney	0.00 RPM	52.50 RPM
SRP017611_liver	0.00 RPM	14.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1340 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1340 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028827	1 retrocopy	retro_cfam_1223,
Canis familiaris	ENSCAFG00000032244	8 retrocopies	retro_cfam_1005, retro_cfam_1066, retro_cfam_1299, retro_cfam_1340 , retro_cfam_1499, retro_cfam_2186, retro_cfam_494, retro_cfam_604,
Homo sapiens	ENSG00000244687	4 retrocopies	retro_hsap_2175, retro_hsap_2440, retro_hsap_2884, retro_hsap_4192,
Macaca mulatta	ENSMMUG00000012228	6 retrocopies	retro_mmul_1722, retro_mmul_2382, retro_mmul_351, retro_mmul_436, retro_mmul_629, retro_mmul_907,
Oryctolagus cuniculus	ENSOCUG00000026172	4 retrocopies	retro_ocun_1450, retro_ocun_1481, retro_ocun_454, retro_ocun_539,
Otolemur garnettii	ENSOGAG00000025894	12 retrocopies	retro_ogar_1381, retro_ogar_1391, retro_ogar_153, retro_ogar_1637, retro_ogar_1929, retro_ogar_2027, retro_ogar_2478, retro_ogar_2984, retro_ogar_3172, retro_ogar_3338, retro_ogar_620, retro_ogar_80,
Pan troglodytes	ENSPTRG00000013615	1 retrocopy	retro_ptro_64,
Rattus norvegicus	ENSRNOG00000025580	21 retrocopies	retro_rnor_1014, retro_rnor_1032, retro_rnor_1291, retro_rnor_1609, retro_rnor_1649, retro_rnor_1650, retro_rnor_1651, retro_rnor_2055, retro_rnor_2282, retro_rnor_2406, retro_rnor_2407, retro_rnor_2412, retro_rnor_2488, retro_rnor_2489, retro_rnor_2490, retro_rnor_2534, retro_rnor_2535, retro_rnor_2905, retro_rnor_819, retro_rnor_881, retro_rnor_991,
Ictidomys tridecemlineatus	ENSSTOG00000014322	6 retrocopies	retro_itri_1001, retro_itri_1002, retro_itri_1134, retro_itri_1452, retro_itri_1600, retro_itri_992,