RetrogeneDB ID: retro_cfam_287

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:6872772..6873261(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000034
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TEX35
• Ensembl ID: ENSCAFG00000014010
• Aliases: None
• Description: testis expressed 35 [Source:HGNC Symbol;Acc:25366]

Sequence

>retro_cfam_287
CAGACATATGACTACAAAGGAGCGAAACAAGATGGGCCATTTACCAAACCAGGAGGGACACATGAGCTAAGGAATGAACT
CAGGGAGGTGAGGGAAGAGCTCAAGATAAAAATGAGGAGATCAAACAGATAAAGGGCGTAATGGACAAGGATTTTGATAA
ACTCCAGGAATTTGTGGAGATTATGAAGGAAATGCAGAAGGATATGGACGAGAAGATGGATGTTTTAATAAATATACAGA
AGAACAGCAAGCTTCCCCTTAGAAGAGGGCCAAAGGAACAGCAGGAACTCAGACTGATAGGAAAAACAGACATAGACCCC
CAGCTCCGGCTCAAGAAAATGGATGGAGCAGATGGAACACCACTTTCTCTTCACAAGAAGATCATGGCCCTACAAAAGAC
AAAGAAGGACCCTCTGGATTCCCTTCATCAATGCGGGACCTACTGCGAAAAATGTTTGTTGAGTGCCCTAAAGAACAACT
ACAATCAGG

Alignment

ORF - retro_cfam_287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.55 %
• Parental protein coverage: 71.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTYDYKGAKQDGPFTKPGGTHELRNELREVREELKEKM-DEIKQIKGVMDKDFDKLQEFVEIMKEMQKDM
          QTYDYKGAKQDGPFTKPGGTHELRNELREVREELK.KM..EIKQIKGVMDKDFDKLQEFVEIMKEMQKDM
Retrocopy QTYDYKGAKQDGPFTKPGGTHELRNELREVREELKIKM<EEIKQIKGVMDKDFDKLQEFVEIMKEMQKDM

Parental  DEKMDVLINIQKNSKLPLRRGPKEQQELRLIGKTDTDPQLRLKKMDGADGTPLSLHKKIMALQKTKKDPL
          DEKMDVLINIQKNSKLPLRRGPKEQQELRLIGKTD.DPQLRLKKMDGADGTPLSLHKKIMALQKTKKDPL
Retrocopy DEKMDVLINIQKNSKLPLRRGPKEQQELRLIGKTDIDPQLRLKKMDGADGTPLSLHKKIMALQKTKKDPL

Parental  DSLHQCGTCCDKCFVSALKN-TTIR
          DSLHQCGT.C.KC..SALKN.TTIR
Retrocopy DSLHQCGTYCEKCLLSALKN>TTIR

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	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_287 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_287 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014010	1 retrocopy	retro_cfam_287 ,