RetrogeneDB ID: retro_cfam_1944

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:23701454..23702049(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KDELR2
• Ensembl ID: ENSCAFG00000015746
• Aliases: None
• Description: KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2 [Source:HGNC Symbol;Acc:6305]

Sequence

>retro_cfam_1944
TCCCACCTCCTAGCCATCATCTTGCCACTGCTCACAACCTGGAAGTCCGGCTCTTGTGCGGGGATTTCAGGGAAGAGCCA
GGTCCTGTTTGCTGTGTTCACTGGCCGGTACCTGGACCTCTTCACCAACTGCATCTCACTGTACAACAGGTGCATGAAGG
TGGTCTGCACTGCCTGATCCTTCACCACAGTCTGGCTGATTTACAGCAAGTTCAAAGCCACTTAGGATGGGAACCATGAC
ACATTCCGAGTGGAGTTCCCCGTTGTTCCCACGGCCATCCTGGCATTCCTGGTCAACCATGACTTCACCCTCTAGAGGTC
CTCTGGACCTTCTCCATCTACCTGGGGTCGGTAGCCATCCTGCCGCAGCCGTTCACGGTGAGCAAGAGGGCGGAGGCCGA
GACCATCCCCAGCCACTGCCCGTTTGCTCTGGGCGTCCACCGCTGCTTTCTCGCTTCCACTGGCTCTGGCGCTACCTCTC
CGAGGGCTTCTTCGACCTCATTGCCATCGTAGCAGGCCTAGTCCAGACTGTCCTCTACTGCGATTCCTTCCACCTCTACA
TCACCAAAGTCCTGAAGGGGAAGGAGCGGAGTTTG

Alignment

ORF - retro_cfam_1944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.81 %
• Parental protein coverage: 94.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SHLAAIVILLLKIWKTRSCAGISGKSQLLFALVFTTRYLDLFTSFISLYNTSMKLIYIACSYATVYLIYM
          SHL.AI...LL..WK..SCAGISGKSQ.LFA.VFT.RYLDLFT..ISLYN..MK....A.S..TV.LIY.
Retrocopy SHLLAIILPLLTTWKSGSCAGISGKSQVLFA-VFTGRYLDLFTNCISLYNRCMKVVCTA*SFTTVWLIYS

Parental  KFKATYDGNHDTFRVEFLVVPVGGLSFLVNHDFS-PLEILWTFSIYLESVAILPQLFMISKTGEAETITT
          KFKAT.DGNHDTFRVEF.VVP...L.FLVNHDF..PLE.LWTFSIYL.SVAILPQ.F..SK..EAETI..
Retrocopy KFKAT*DGNHDTFRVEFPVVPTAILAFLVNHDFT<PLEVLWTFSIYLGSVAILPQPFTVSKRAEAETIPS

Parental  HYLFFLGLYRA-LYLVNWIWRFYFEGFFDLIAVVAGVVQTILYCDFFYLYITKVLKGKKLSL
          H..F.LG..R..L....W.WR...EGFFDLIA.VAG.VQT.LYCD.F.LYITKVLKGK..SL
Retrocopy HCPFALGVHRC<LSRFHWLWRYLSEGFFDLIAIVAGLVQTVLYCDSFHLYITKVLKGKERSL

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	0.08 RPM	63.42 RPM
SRP017611_brain	0.08 RPM	40.81 RPM
SRP017611_kidney	0.20 RPM	123.36 RPM
SRP017611_liver	0.07 RPM	77.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1944 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1944 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1944 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015746	2 retrocopies	retro_cfam_1944 , retro_cfam_318,
Choloepus hoffmanni	ENSCHOG00000000125	1 retrocopy	retro_chof_2624,
Dasypus novemcinctus	ENSDNOG00000009897	1 retrocopy	retro_dnov_2654,
Echinops telfairi	ENSETEG00000016544	1 retrocopy	retro_etel_1867,
Monodelphis domestica	ENSMODG00000007832	1 retrocopy	retro_mdom_1547,