RetrogeneDB ID: retro_cfam_776

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:36535784..36536309(-)
• Located in intron of: ENSCAFG00000007149

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERCC1
• Ensembl ID: ENSCAFG00000004448
• Aliases: None
• Description: excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence) [Source:HGNC Symbol;Acc:3433]

Sequence

>retro_cfam_776
CAGAGGGGCAACCCTGTGCTGAAGTTTGTGCGGAATGTGCCCTGGGAATTTGGTGACGTGCTTCCCGACTATGTGCTGGG
CCAGAGCACCTGTGCCCTGTTCCTCAGCCTCCGCTACCACAATCTCCACCCGGACTACCTCCACGAGCGGCTGCAGAGCC
TGGGGAAGAGTTTTGCGCTGCGGGTCCTGCTGGTCCAGGTGGACGTGAAAGATCCTCAGCAGGCCCTCAAGGAGCTGGCT
AAGATGTGCATCCTGGCCTACTGCACCCTGGTCCTCGCCTGGAGCCCCGAGGAGGCTGGGCGGTACCTGGAGACTTACAA
AGCCTATGAGCAGAAGCCGGCCAACCTCCTGATGGAGAAGCTGGAGCAGGACTTCGTCTCCCGGGTGACTGAATGCCTGA
CCACCGTGAAGTCAGTCAATAAAACAGACAGCCAGACCCTCCTGACAACTTTTGGGTCTCTGGAACAGCTCATGACCGCA
TCGAGGGAAGATCTGGCTTTGTGTCCAGGCCTGGGGCCCCAGAAG

Alignment

ORF - retro_cfam_776 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.71 %
• Parental protein coverage: 54.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRGNPVLKFVRNVPWEFGDVLPDYVLGQSTCALFLSLRYHNLHPDYIHERLQSLGKSFALRVLLVQVDVK
          QRGNPVLKFVRNVPWEFGDVLPDYVLGQSTCALFLSLRYHNLHPDY.HERLQSLGKSFALRVLLVQVDVK
Retrocopy QRGNPVLKFVRNVPWEFGDVLPDYVLGQSTCALFLSLRYHNLHPDYLHERLQSLGKSFALRVLLVQVDVK

Parental  DPQQALKELAKMCILADCTLVLAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVN
          DPQQALKELAKMCILA.CTLVLAWSPEEAGRYLETYKAYEQKPA.LLMEKLEQDFVSRVTECLTTVKSVN
Retrocopy DPQQALKELAKMCILAYCTLVLAWSPEEAGRYLETYKAYEQKPANLLMEKLEQDFVSRVTECLTTVKSVN

Parental  KTDSQTLLTTFGSLEQLMAASREDLALCPGLGPQK
          KTDSQTLLTTFGSLEQLM.ASREDLALCPGLGPQK
Retrocopy KTDSQTLLTTFGSLEQLMTASREDLALCPGLGPQK

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	0.71 RPM	12.77 RPM
SRP017611_brain	0.00 RPM	11.04 RPM
SRP017611_kidney	0.26 RPM	16.18 RPM
SRP017611_liver	0.00 RPM	6.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_776 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_776 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_776 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014643	2 retrocopies	retro_acar_17, retro_acar_175,
Canis familiaris	ENSCAFG00000004448	1 retrocopy	retro_cfam_776 ,