RetrogeneDB ID: retro_cfam_316

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:67721857..67722685(-)
• Located in intron of: ENSCAFG00000001106

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC6
• Ensembl ID: ENSCAFG00000019317
• Aliases: None
• Description: THO complex 6 homolog (Drosophila) [Source:HGNC Symbol;Acc:28369]

Sequence

>retro_cfam_316
AAGAAGCCAGTGGTGACATTCCAAGCCCATGATGGGCCGGTCTACAGCATGGTCTCCACGGATCGACATCTGCTCAGTGC
TGGGGATGGGGAAGTGAAGGCCTGGCTTTGGGCAGAGATCCTCAAGAAGGGTTGTAAGGAGCTGTGGCAGCGTCAGCCCC
CATACAGGACCAGCCTAGAAGTGCCTGAGATCAATGCTTTGCTTCTCGTCCCCAAGGAGAATTCTCTCATCCTGGCAGGG
GGAGACTGTCAGTTGCATACGATGGACCTTGAGACCGGGACCTTCACACGGGCCCTCCGGGGCCACACAGACTATGTCCA
CTGCCTGGCACTGCGGGAGCGGAGTCCTGAGGTGCTGTCAGGTGGAGAGGATGGAGCCGTGCGACTTTGGGACCTCCGCA
CAGCCAAGGAAGTCCAGACCATTGAGGTATGTAAGCATGAGGAGTGCTCGAGGCCACACAATGGGCGTTGGATCGGCTGT
TTGGCCACTGACTCAGACTGGATGGTCTGTGGAGGAGGCCCAGCACTCACCCTCTGGCACCTCCGATCCTCCACACCCAC
AACTATTTTCCCCATACGGGCGCCACAGAAACACGTCACCTTCTACCAGGACCTGATTCTGTCAGCTGGCCAGGGCCTCT
GTGTCAACCAGTGGCAGCTGAGTGGGGAGCTCAAGGCGCAGGTGCCTGGCTCCTCCCTAGGGCTGCTCAGCCTCAGTCTC
AACCAGCAGCCAGCAGCACCCGAGTGCAAGGTCCTGACAGACACAGGTAACAGCTGCCGCATGGATGTCTTCACGAATCT
CGGCTACCGCGCCTTCCCCTTGTCCTTC

Alignment

ORF - retro_cfam_316 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.01 %
• Parental protein coverage: 80.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKPVVTFQAHDGPVYSMVSTDRHLLSAGDGEVKAWLWAEILKKGCKELWRRQPPYRTSLEVPEINALLLV
          KKPVVTFQAHDGPVYSMVSTDRHLLSAGDGEVKAWLWAEILKKGCKELW.RQPPYRTSLEVPEINALLLV
Retrocopy KKPVVTFQAHDGPVYSMVSTDRHLLSAGDGEVKAWLWAEILKKGCKELWQRQPPYRTSLEVPEINALLLV

Parental  PKENSLILAGGDCQLHTMDLETGTFTRALRGHTDYVHCLALRERSPEVLSGGEDGAVRLWDLRTAKEVQT
          PKENSLILAGGDCQLHTMDLETGTFTRALRGHTDYVHCLALRERSPEVLSGGEDGAVRLWDLRTAKEVQT
Retrocopy PKENSLILAGGDCQLHTMDLETGTFTRALRGHTDYVHCLALRERSPEVLSGGEDGAVRLWDLRTAKEVQT

Parental  IEVYKHEECSRPHNGRWISCLATDSDWMVCGGGPALTLWHLRSSTPTTIFPIRVPQKHVTFYQDLILSAG
          IEV.KHEECSRPHNGRWI.CLATDSDWMVCGGGPALTLWHLRSSTPTTIFPIR.PQKHVTFYQDLILSAG
Retrocopy IEVCKHEECSRPHNGRWIGCLATDSDWMVCGGGPALTLWHLRSSTPTTIFPIRAPQKHVTFYQDLILSAG

Parental  QGRCVNQWQLSGELKAQVPGSSPGLLSLSLNQQPAAPECKVLTAAGNSSRVDVFTNLGYRAFSLSF
          QG.CVNQWQLSGELKAQVPGSS.GLLSLSLNQQPAAPECKVLT..GNS.R.DVFTNLGYRAF.LSF
Retrocopy QGLCVNQWQLSGELKAQVPGSSLGLLSLSLNQQPAAPECKVLTDTGNSCRMDVFTNLGYRAFPLSF

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	14.91 RPM
SRP017611_brain	0.00 RPM	8.26 RPM
SRP017611_kidney	0.00 RPM	7.99 RPM
SRP017611_liver	0.00 RPM	4.57 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_316 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_316 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	ENSCAFG00000019317	1 retrocopy	retro_cfam_316 ,