RetrogeneDB ID: retro_cfam_966

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:42198835..42199698(+)
• Located in intron of: ENSCAFG00000013719

Retrocopy information

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

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_966
ATGAGCGACAGCGGCGAGCAGAACTACGGCAGCGGGAATCCTGCTCTGCTTCCAGAAGTGGAAGTGCTCATGGATCTGGG
AAATCTGCAAGGCATACCCCTGCAAGGTCTCGCTCCAAGGAAGATTCCAGGCGTTCCAGATCAAAGTCCAGGTCCAGACC
TGAATCTAGGTCTAGACCCAGAAGAAGTTCTCGAAGGCATTATACAAGATCAAGATCCCGCTCCCGCTCCCATAGACTAT
CCCATAGCAGGTCTTACAGTCGAGATTATGGAAGACGGCATAGCCACAGTCACTCTCCCATGTCTACTCGCAGGCGTCAT
GTTGGGAATCGGGCAAATCCCGACCCCAACTGCTGTTGTGGAGTATTTGGATTGAGCTTGTACACTACAGAAAGAGATCT
AAGAGAAGTGTTCTCTAAATATGGCCCCATTGCTGACGTGTCTATTGTATATGACCAGCAATCTAGGCGTTCCAGAGGAT
TTGCCTTTGTATATTTTGAAAATGTAGACGATGCCAAGGAAGCAAAAGAGTGTGCCAATGGAATGGAGTTTGATGGACGT
AGGATCAGAGTTGATTTCTCTATAACAAAAAGACCACATAACCCAACACCAGAAATTTACATGGGGAGACCTACCTATGG
CAGCTCACACCGTCGGGATTACTGTGACAGAGGATATGATCGAGGCTATGATGATCGTGACTACTATAGCAGATCATACA
GAGGAAGTGGTGGAGGAGGAAGAGGATGGAGAACTGCTCAAGATAGGGATCATATTTACAGAAAGCGGTCACCTTCTCCT
TACTATAGTCGTGGAGGATACAGATCGTGTTCTAGATCTCGATCATACTCACCTCATCACTAT

Alignment

ORF - retro_cfam_966 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDSGEQNYG-ERESRSASRSGSAHGSGKSARHTPARSRSKEDSRRSRSKSRSRSESRSRSRRSSRRHYT
          MSDSGEQNYG..RES.SASRSGSAHGSGKSARHTPARSRSKEDSRRSRSKSRSR.ESRSR.RRSSRRHYT
Retrocopy MSDSGEQNYG<QRESCSASRSGSAHGSGKSARHTPARSRSKEDSRRSRSKSRSRPESRSRPRRSSRRHYT

Parental  RSRSRSRSHRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFS
          RSRSRSRSHR.S.SRSYSRDY.RRHSHSHSPMSTRRRHVGNRANPDPNCC.GVFGLSLYTTERDLREVFS
Retrocopy RSRSRSRSHRLSHSRSYSRDYGRRHSHSHSPMSTRRRHVGNRANPDPNCCCGVFGLSLYTTERDLREVFS

Parental  KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMG
          KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE.ANGME.DGRRIRVDFSITKRPH.PTP.IYMG
Retrocopy KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKECANGMEFDGRRIRVDFSITKRPHNPTPEIYMG

Parental  RPTYGSSRRRDYYDRGYDRGYDDRDYYSRSYRGGGGGGGGWRAAQDRDQIYRRRSPSPYYSRGGYRSRSR
          RPTYGSS.RRDY.DRGYDRGYDDRDYYSRSYRG.GGGG.GWR.AQDRD.IYR.RSPSPYYSRGGYRS.SR
Retrocopy RPTYGSSHRRDYCDRGYDRGYDDRDYYSRSYRGSGGGGRGWRTAQDRDHIYRKRSPSPYYSRGGYRSCSR

Parental  SRSYSPRKF
          SRSYSP...
Retrocopy SRSYSPHHY

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	75.35 RPM
SRP017611_brain	0.00 RPM	26.20 RPM
SRP017611_kidney	0.00 RPM	42.53 RPM
SRP017611_liver	0.44 RPM	17.04 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_966 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_966 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_966 has 0 orthologous retrocopies within eutheria group .

---

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,