RetrogeneDB ID: retro_cfam_657

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:22686673..22686989(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6ORF57
• Ensembl ID: ENSCAFG00000002602
• Aliases: None
• Description: None

Sequence

>retro_cfam_657
ATGACTGGATCAGGGCTAGTTCAGTTACTCGGCTGCATCCTGGCCACTGTGTGGTCAGTGGCAAGATCACCCCTTCTGTG
TCATATTGTGAGGAGAATGAGTTCTCAAGGAGAAAAACCCAAACACAATTAAACAATCTCTTAAGAAGTTACCAGAAGGT
CATTTTGATGGACCAGAAGATTCTAATTTAGAAAAAGTACCACTAATAAAATTTCCAAGTTATGTTAATCCTGTTACCAA
AGAAAAAGGTGGACCCAGAAGCCCTGAAACTGCCTGATATGGAGATTAGAAATGAGAAAGACACTGTATTGATTTT

Alignment

ORF - retro_cfam_657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTVSRLARLLGCVPATAWRAARSPLLCHSVRKMSSQGEKSK-PIQQSLKKPKLPEGRFDAPEDSNLEKEP
          MT.S.L..LLGC..AT.W..ARSPLLCH.VR.MSSQGEK.K..I.QSLKK..LPEG.FD.PEDSNLEK.P
Retrocopy MTGSGLVQLLGCILATVWSVARSPLLCHIVRRMSSQGEKPK>TIKQSLKK--LPEGHFDGPEDSNLEKVP

Parental  LTKFPDDINPVTKEKGGPRGPEPTRYGDWERKGRCIDF
          L.KFP...NPVTKEKGGPR.PE...YGD......CIDF
Retrocopy LIKFPSYVNPVTKEKGGPRSPETA*YGD*K*ERHCIDF

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	10.84 RPM
SRP017611_brain	0.00 RPM	6.75 RPM
SRP017611_kidney	0.00 RPM	20.54 RPM
SRP017611_liver	0.00 RPM	3.63 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_657 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_657 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_657 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002602	2 retrocopies	retro_cfam_268, retro_cfam_657 ,
Choloepus hoffmanni	ENSCHOG00000011410	6 retrocopies	retro_chof_176, retro_chof_1854, retro_chof_252, retro_chof_465, retro_chof_694, retro_chof_966,
Erinaceus europaeus	ENSEEUG00000011260	1 retrocopy	retro_eeur_539,
Echinops telfairi	ENSETEG00000011154	1 retrocopy	retro_etel_1362,
Felis catus	ENSFCAG00000026799	1 retrocopy	retro_fcat_986,
Rattus norvegicus	ENSRNOG00000028087	1 retrocopy	retro_rnor_1514,
Tupaia belangeri	ENSTBEG00000004344	2 retrocopies	retro_tbel_3788, retro_tbel_4408,
Tarsius syrichta	ENSTSYG00000001769	1 retrocopy	retro_tsyr_67,