RetrogeneDB ID: retro_cfam_1971

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:10447459..10447916(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000013395
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRA2B
• Ensembl ID: ENSCAFG00000013345
• Aliases: None
• Description: transformer 2 beta homolog (Drosophila) [Source:HGNC Symbol;Acc:10781]

Sequence

>retro_cfam_1971
GTGTTCTCTAAATATGGCCCCATTGCTGATGTGTCTATTGATATGACCAGCAATCTAGGCGTTCCAGAGGATTTGCCTTT
GTATATTTTGAAAATATAGATGATGCCAAGGAAGCAAAAGAGCATGCCAATGGACTGGAGCTTGATGGACGTAGGATCAG
AGTTGATTTCTCTATAACAAAAAGACCACATACCCCAACACCAGGAATTTACATGGGGAGACCTACCTATGGCAACTCAC
GCCGTCGGGATTACTATGACAGAGGATATATGATCGAGGCTATGATGATCGTGACTACCATAGCAGATCATACAGAGGAG
GTGGTGGAGGAGGAGGAGGATGGAGAGCTGCTCAAGATAGGGATAAGATTTACAGAAGGCAGTCACCTTCTCCTTACTAT
AGTCGTGGAGGATACAGATCACGTTCTAGATCTCGATTGTACTCACCTTGTCGCTAT

Alignment

ORF - retro_cfam_1971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 52.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFSKYGPIADVSIV-YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPG
          VFSKYGPIADVSI..YDQQSRRSRGFAFVYFEN.DDAKEAKE.ANG.ELDGRRIRVDFSITKRPHTPTPG
Retrocopy VFSKYGPIADVSID<YDQQSRRSRGFAFVYFENIDDAKEAKEHANGLELDGRRIRVDFSITKRPHTPTPG

Parental  IYMGRPTYGSS-RRRDYY-DRGYDRGYDDRDYYSRSYRGGGGGGGGWRAAQDRDQIYRRRSPSPYYSRGG
          IYMGRPTYG.S.RR..Y...R.YDRGYDDRDY.SRSY............AQDRD.IYRR.SPSPYYSRGG
Retrocopy IYMGRPTYGNSRRRDYYD<QRIYDRGYDDRDYHSRSYXXXXXXXXXXXXAQDRDKIYRRQSPSPYYSRGG

Parental  YRSRSRSRSYSPRKF
          YRSRSRSR.YSP...
Retrocopy YRSRSRSRLYSPCRY

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	0.76 RPM	75.35 RPM
SRP017611_brain	0.87 RPM	26.20 RPM
SRP017611_kidney	0.40 RPM	42.53 RPM
SRP017611_liver	1.31 RPM	17.04 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1971 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1971 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1971 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013345	2 retrocopies	retro_cfam_1971 , retro_cfam_966,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Cavia porcellus	ENSCPOG00000006313	1 retrocopy	retro_cpor_162,
Rattus norvegicus	ENSRNOG00000001783	4 retrocopies	retro_rnor_1130, retro_rnor_1915, retro_rnor_2156, retro_rnor_2807,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,