RetrogeneDB ID: retro_cfam_1175

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 25:6366482..6367102(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000006268
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FEZ1
• Ensembl ID: ENSCAFG00000010910
• Aliases: None
• Description: fasciculation and elongation protein zeta 1 (zygin I) [Source:HGNC Symbol;Acc:3659]

Sequence

>retro_cfam_1175
TTCGAGTCTGTGGAGGACCTCGTGAATGAATTTGAGGAGAAGCTCAATGTCTGCTTTCGGAACTACAATGCCAAGACGGA
GACCCTAGCTCCCGTGAAGAACCAGTTCCAGATCCAAGAGGAGGAGGAGACCCTGCAGGATGAGGAGGCTTGGGATGCTC
TGACAGACAATTACATCCCTTCACTCTCAGAAGGCCGGAGGGACCCAAACATGGAGGCTCTGAATGGCAACAGCTCTGAC
ACTGAGATCCACGAGAAAGAAGAGGAAGAGCTGGATGAGAAGAGTGAACGTGATTCTGGCATCAATGAGGAGCCTCTACT
CACAGCAGATCAGGTGATTGAGGAGACTGAAGAAATGATGCAGAACTCCCCAGACCCTGAGGAAGAAGAGGAGGTTCTGG
AAGAGGAGGAGAAGGGAGAAACCTCCTCCCAGGCAGCCTCGGTCCTCCTGCAGGAGATGCGGGTCTTGACCCAGACCTTC
AACAACGACTGGTCCTACAAAGGCCTGAGGCACATGTCGGGGTCGGAGCTGACCGAGCTGCTGGACCAGGTGGAGGGCGC
CACCCCGGCTTCTCGGAGGAGCTGGTGCAGCTGGAGTTTGAGGAGGAAGAGAACTCCTTC

Alignment

ORF - retro_cfam_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.58 %
• Parental protein coverage: 52.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FKSMEDLVNEFDEKLNVCFRNYNAKTETLAPVKNQFQIQEEEETLQDEEVWDALTDNYIPSLSEDWRDPN
          F.S.EDLVNEF.EKLNVCFRNYNAKTETLAPVKNQFQIQEEEETLQDEE.WDALTDNYIPSLSE..RDPN
Retrocopy FESVEDLVNEFEEKLNVCFRNYNAKTETLAPVKNQFQIQEEEETLQDEEAWDALTDNYIPSLSEGRRDPN

Parental  MEALNGNSSDTEIHEKEEEEFNEKSEHDSGINEEPLLTADQVIEEIEEMMQNSPDPEEEEEVLEEEDEGE
          MEALNGNSSDTEIHEKEEEE..EKSE.DSGINEEPLLTADQVIEE.EEMMQNSPDPEEEEEVLEEE..GE
Retrocopy MEALNGNSSDTEIHEKEEEELDEKSERDSGINEEPLLTADQVIEETEEMMQNSPDPEEEEEVLEEEEKGE

Parental  TSSQADSVLLQEMQALTQTFNNNWSYEGLRHLSGSELTELLDQVEGAI-RDFSEELVQQLARRDELEF
          TSSQA.SVLLQEM..LTQTFNN.WSY.GLRH.SGSELTELLDQVEGA....FSEELVQ......E..F
Retrocopy TSSQAASVLLQEMRVLTQTFNNDWSYKGLRHMSGSELTELLDQVEGAT<PGFSEELVQLEFEEEENSF

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	291.43 RPM
SRP017611_brain	0.48 RPM	231.59 RPM
SRP017611_kidney	0.13 RPM	39.56 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_1175 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1175 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	ENSCAFG00000010910	1 retrocopy	retro_cfam_1175 ,