RetrogeneDB ID: retro_cfam_1223

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:22066364..22066799(+)
• Located in intron of: ENSCAFG00000011421

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V2
• Ensembl ID: ENSCAFG00000028827
• Aliases: None
• Description: Canis lupus familiaris ubiquitin-conjugating enzyme E2 variant 2 (UBE2V2), mRNA. [Source:RefSeq mRNA;Acc:NM_001205115]

Sequence

>retro_cfam_1223
ATGGCAGTCTCCACAGGTGTTAAAGTTCCTTGTAATTTTCGCTTGTTGGAAGAACTTGAAGAAGGACAAAAAGGAGTAGG
CGATGGTACGGTTAGCTGGGGCCTTGAAGATAATGAAGATATGACACTTACAAGGTGGACAGGCATGATTATTGGGCCAC
CAAGGACAAATTATGAAAACAGAATATATAGCCTGAAAGTAGAACGTGGACCTAAATACCCAGAAGCTCCTCCATCAGTT
AGATTTGTAACCAAAATTAATATGAATGGAATTAATAATTCCAGTGGAATGGTGGATGCACGGAGCATACCAGTGTTAGC
TAAATGGCAAAATTCATATAGCATTAAAGTTGTACTTCAAGAGCAAAGACGTCTAATGATGTCCAAAGAAAATATGAAGC
TTCCACAGCCACCAGAAGGACAAACATACAACAAT

Alignment

ORF - retro_cfam_1223 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECG
          MAVSTGVKVP.NFRLLEELEEGQKGVGDGTVSWGLED.EDMTLTRWTGMIIGPPRTNYENRIYSLKVE.G
Retrocopy MAVSTGVKVPCNFRLLEELEEGQKGVGDGTVSWGLEDNEDMTLTRWTGMIIGPPRTNYENRIYSLKVERG

Parental  PKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEG
          PKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQE.RRLMMSKENMKLPQPPEG
Retrocopy PKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQEQRRLMMSKENMKLPQPPEG

Parental  QTYNN
          QTYNN
Retrocopy QTYNN

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	48.76 RPM
SRP017611_brain	0.16 RPM	44.54 RPM
SRP017611_kidney	0.20 RPM	37.71 RPM
SRP017611_liver	0.00 RPM	12.76 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1223 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1223 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 67 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,
Cavia porcellus	ENSCPOG00000014413	4 retrocopies	retro_cpor_1277, retro_cpor_540, retro_cpor_751, retro_cpor_849,
Felis catus	ENSFCAG00000007602	6 retrocopies	retro_fcat_1169, retro_fcat_1256, retro_fcat_141, retro_fcat_15, retro_fcat_1678, retro_fcat_1868,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Myotis lucifugus	ENSMLUG00000002057	6 retrocopies	retro_mluc_1077, retro_mluc_2371, retro_mluc_386, retro_mluc_559, retro_mluc_659, retro_mluc_985,
Macaca mulatta	ENSMMUG00000008223	1 retrocopy	retro_mmul_1066,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979, retro_mdom_736, retro_mdom_786, retro_mdom_979,
Mustela putorius furo	ENSMPUG00000001010	2 retrocopies	retro_mputfur_460, retro_mputfur_979,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Tupaia belangeri	ENSTBEG00000015720	27 retrocopies	retro_tbel_1333, retro_tbel_1456, retro_tbel_1479, retro_tbel_1551, retro_tbel_160, retro_tbel_1740, retro_tbel_1784, retro_tbel_2129, retro_tbel_2149, retro_tbel_2317, retro_tbel_2334, retro_tbel_2496, retro_tbel_2890, retro_tbel_2935, retro_tbel_3021, retro_tbel_3102, retro_tbel_3141, retro_tbel_3461, retro_tbel_3573, retro_tbel_3734, retro_tbel_3935, retro_tbel_3971, retro_tbel_4227, retro_tbel_4319, retro_tbel_4720, retro_tbel_640, retro_tbel_909,