RetrogeneDB ID: retro_cfam_685

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:38681011..38681459(-)
• Located in intron of: ENSCAFG00000006596

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGN
• Ensembl ID: ENSCAFG00000014821
• Aliases: None
• Description: None

Sequence

>retro_cfam_685
CCAGTGTGGAAGGAGGCATCCACCTCTCTGATCTTTGTAGATATTTCTGCAAAAAAGGTTTGCCAGTAGGATTTGCTCAG
CAAGTGAGTGCAGCAAGTGACCATGGATTCCCCCATCAGCTCTGTGACCCTTCACCAGGCAGGAGGTTATGTTGCCACCA
TTGGAACAAAGTTCTGTGCTTTGAACTGGGAAGATCAGTTAACAGTTGTCCTGGCCACAGTAGATAAGAGAAAAACAATC
AGTTCAATGATGGGAAGCTGGATCCCACTGGGAGATACTTTGCTGGCACCATGCTTGAGGAAATGATGCCAGCAGTTCTG
GAGCAACACCAGGGGTTCCTGTACTCCCTTTTTCTGACCACCACGCAGTAGAGCACTTTGACCAGGTAGACATCTACAGT
GATTTGGATTGGTCCCTGGATCACAAAATCATCTATTACATTGACAGC

Alignment

ORF - retro_cfam_685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.55 %
• Parental protein coverage: 50.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVWEEAANSLLFVDIPAKKVCRWDSLSKSVQHVTVDAPISSVALRQGRGYVATIGTKFCALNWEDQSAVA
          PVW.EA..SL.FVDI.AKKVC..D.LSK.VQ.VT.D.PISSV.L.Q..GYVATIGTKFCALNWEDQ..V.
Retrocopy PVWKEASTSLIFVDISAKKVCQ*DLLSK*VQQVTMDSPISSVTLHQAGGYVATIGTKFCALNWEDQLTVV

Parental  LATVDK-DKKNNRFNDGKVDPAGRYFAGTMAEETAPAVLERHQGSLYSL-FPDGHVEKYFDQVDISNGLD
          LATVDK..K.N..FNDGK.DP.GRYFAGTM.EE..PAVLE.HQG.LYSL.F.D.H....FDQVDI...LD
Retrocopy LATVDK<EKNN-QFNDGKLDPTGRYFAGTMLEEMMPAVLEQHQGFLYSL<FSDHHAVEHFDQVDIYSDLD

Parental  WSLDHKIFYYIDS
          WSLDHKI.YYIDS
Retrocopy WSLDHKIIYYIDS

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	1.81 RPM
SRP017611_brain	0.00 RPM	0.95 RPM
SRP017611_kidney	0.00 RPM	597.37 RPM
SRP017611_liver	0.00 RPM	365.54 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_685 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_685 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013028	1 retrocopy	retro_amel_915,
Canis familiaris	ENSCAFG00000014821	1 retrocopy	retro_cfam_685 ,
Monodelphis domestica	ENSMODG00000000375	1 retrocopy	retro_mdom_1797,
Mustela putorius furo	ENSMPUG00000013105	1 retrocopy	retro_mputfur_1618,