RetrogeneDB ID: retro_cfam_1517

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 33:3860036..3860678(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008414
• Aliases: None
• Description: None

Sequence

>retro_cfam_1517
CAGTTCGACTTGCAGGAAATCTTCTCCTCAATCCTGAAAGAGGTCCTTGACAACCTGAAGAGATCTGAATACTTCTGCTT
CCTCTAGTTCCTGCACCGTGAGAACGTCAGCATCATCTCCCACACCAACAAGCCCCCCTCCTCTTCAGCCAACTGGTTTT
GGGACTCTGCCATCAAATTCTATTTACTGGAGTTCTTGCTCTGGATCAGCTCCTTCCTGCTGGGCCTCGTTGGCTGATTC
AATGGCTTTTTCTGCTGGCTCCTGTTCATCAGGAAGGAGAGTAACAACTTCAGCTATAAGATCTCCACCTATGAGTGTGG
CTTCAAGCAGCACATCAACGACGGGGCCATCCCCAGAGAGAAGACCACAGAGACCCTGTTGGAGCTGAAGGACTTGCTGG
AGACCCATCCCAAGATGGTGGCCCATTACCCTGTGGAGGTGCTTCATCTCCCTGGGATGACATCTTGCTGAGCTCCTGCT
TCCAAAGGGACAGCTTCTAGATGAACATCATTATGCACAGGCCCTGTGGCAAGGAAGTGCCACAGCTGGACTACTGGCAG
GCCTAGGAGACCATCATGAAGATGGCACAGGGGCAGGCCCCACTGGGCCCAGGCCCACAACTGTGCCATAAAGGACTTTA
AA

Alignment

ORF - retro_cfam_1517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.54 %
• Parental protein coverage: 50.45 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QFHLQEISFPSTLEEVLNNLDSHLKKSEYFRFLWFPHSENVSVIYQDHTNKPPSSSANWFWDYAIGFYLL
          QF.LQEI.F.S.L.EVL.N....LK.SEYF.FL.F.H.ENVS.I...HTNKPPSSSANWFWD.AI.FYLL
Retrocopy QFDLQEI-FSSILKEVLDN----LKRSEYFCFL*FLHRENVSII--SHTNKPPSSSANWFWDSAIKFYLL

Parental  EFLLWISSFLPGLVGWINRFFFWLLFTRKKESSDLSHKIFTYECRFKQHVQDWAIPREKTKEALLELKAM
          EFLLWISSFL.GLVG..N.FF.WLLF.R.KES...S.KI.TYEC.FKQH..D.AIPREKT.E.LLELK..
Retrocopy EFLLWISSFLLGLVG*FNGFFCWLLFIR-KESNNFSYKISTYECGFKQHINDGAIPREKTTETLLELKDL

Parental  LEAHPKMVAHFPVEVRFTRG-DDILLSPCFQRDSCYMNIIMYRPYGKDVPRLDYWLTYETIMKKV-GGRP
          LE.HPKMVAH.PVEV....G.DDILLS.CFQRDS..MNIIM.RP.GK.VP.LDYW...ETIMK....GRP
Retrocopy LETHPKMVAHYPVEVLHLPG<DDILLSSCFQRDSF*MNIIMHRPCGKEVPQLDYWQA*ETIMKMA>RGRP

Parental  HWAKAHNCTRKDFE
          HWA.AHNC..KDF.
Retrocopy HWAQAHNCAIKDFK

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	0.00 RPM
SRP017611_brain	0.00 RPM	0.40 RPM
SRP017611_kidney	0.00 RPM	0.07 RPM
SRP017611_liver	0.00 RPM	139.81 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1517 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1517 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000147	1 retrocopy	retro_amel_895,
Canis familiaris	ENSCAFG00000008414	1 retrocopy	retro_cfam_1517 ,
Felis catus	ENSFCAG00000023835	1 retrocopy	retro_fcat_1263,