RetrogeneDB ID: retro_cfam_708

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:41010687..41011142(+)
• Located in intron of: ENSCAFG00000006979

Retrocopy information

• Ensembl ID: ENSCAFG00000007015
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GPATCH11
• Ensembl ID: ENSCAFG00000006041
• Aliases: None
• Description: G patch domain containing 11 [Source:HGNC Symbol;Acc:26768]

Sequence

>retro_cfam_708
ATGCTAAGGCAGATCCGAGAAGCCCATCGGAAAGAAGAAAAGCAACAGGAAGCCAATTTGAAAACAGGCAGAAGAGTTTA
AAAGAAGAAGAACAAGAAAGACGTGACATTGGGTTGAAGAATGCTCTAGGCTGTGAAAACAAAGGGTTTACCTTGCTGCA
AAAGATGGGATATAAAAGTGGTCAGCCCCTTGGCAAGAGTGGAGATGGTATTGTTGAGCCAATCCCCCTTAACGTCAAAA
CAGGAAAAAGCGGCCTTGGTCATGAGGCATTACTGAAACAGAAAGCAGAGGAAACACTAGAAAGTTGTAGGAGAAAGATT
CACATGAAAAACCAAGCTGAAGAAACAGCTGCAGAGCAGTTTCGACTGCGACTTAAATATAAGCAAGATGAAGTGAAGCT
GGAAGGGGACCTGAAAAGAAGCCAGCAAGCCTGCCGGCAGTTGGATACACAGAAG

Alignment

ORF - retro_cfam_708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.81 %
• Parental protein coverage: 87.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLRQIREARRKEEKQQEANLK-NRQKSLKEEEQERRDIGLKNALGCENKGFALLQKMGYKSGQALGKSGD
          MLRQIREA.RKEEKQQEANLK.NRQKSLKEEEQERRDIGLKNALGCENKGF.LLQKMGYKSGQ.LGKSGD
Retrocopy MLRQIREAHRKEEKQQEANLK<NRQKSLKEEEQERRDIGLKNALGCENKGFTLLQKMGYKSGQPLGKSGD

Parental  GIVEPIPLNVKTGKSGLGHEALLKRKAEEKLESYRRKIHMKNQAEETAAEQFRLRLKHKQDEVKLEGDLR
          GIVEPIPLNVKTGKSGLGHEALLK.KAEE.LES.RRKIHMKNQAEETAAEQFRLRLK.KQDEVKLEGDL.
Retrocopy GIVEPIPLNVKTGKSGLGHEALLKQKAEETLESCRRKIHMKNQAEETAAEQFRLRLKYKQDEVKLEGDLK

Parental  RSQRACQQLDTQK
          RSQ.AC.QLDTQK
Retrocopy RSQQACRQLDTQK

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	1.09 RPM	9.32 RPM
SRP017611_brain	1.19 RPM	12.07 RPM
SRP017611_kidney	1.98 RPM	15.32 RPM
SRP017611_liver	0.29 RPM	2.61 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_708 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_708 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_708 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006041	1 retrocopy	retro_cfam_708 ,
Choloepus hoffmanni	ENSCHOG00000004377	3 retrocopies	retro_chof_1420, retro_chof_2292, retro_chof_398,
Homo sapiens	ENSG00000152133	1 retrocopy	retro_hsap_2802,
Monodelphis domestica	ENSMODG00000015289	1 retrocopy	retro_mdom_1855,
Nomascus leucogenys	ENSNLEG00000027017	1 retrocopy	retro_nleu_1542,
Pan troglodytes	ENSPTRG00000011832	1 retrocopy	retro_ptro_1899,