RetrogeneDB ID: retro_cfam_318

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:70421911..70422546(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000001208
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_318
ATGAATCTCTTCTGATTCCTGGGAGACCTCTCCCACCTCCTAGCCATCATCTTGCTACCGCTTAAAATCTGGAAGTCCCG
CTCTTGTGCCGGGATTTCAGGGAAGAGCCAGGTCCTGTTTGCTGTGGTGTTCACTGCCCGGTACCTGGACCTCCTCACCA
ACTACATCTCACTGTACAACACGTACATGAAGGTGGTCTACATTGCCTGTTCCTTCACCACAGTCTGGATGATTTACAGC
AAGTTCAAAGCCACTTATGATGGGAACCATGACACATTCCGAGTGGAGTTCCTCGTTGTTCCCACGGCCATCCTGGCATT
CCTGGTCAACCATGACTTTACCCTCTAGAGATCCTCTGGACCTTCTCCATCTACCTGGAGTTGGTAGCCATCCTGCCACA
GCTGTTCACGGTGAGCAAGACGGGGAAGGCAGAGACCATCACCAGCCACTACCTGTTTGCTCTGGGCGTCTACCGCACGC
TTTATCTCTGCAACTGGATCTGGCGCTACCACTTCGAGGGCTTCTTCGACCTCATTGCCATCGTAGCAGGCCTAGTCCAG
ACTGTCCTCTACTGCGATTTCTTCTACCTCTACATCACCAAAGTCCTGAAGGGGAAGAAGCTGAGTTTGCCGGCG

Alignment

ORF - retro_cfam_318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNIFRLTGDLSHLAAIVILLLKIWKTRSCAGISGKSQLLFALVFTTRYLDLFTSFISLYNTSMKLIYIAC
          MN.F...GDLSHL.AI..L.LKIWK.RSCAGISGKSQ.LFA.VFT.RYLDL.T..ISLYNT.MK..YIAC
Retrocopy MNLF*FLGDLSHLLAIILLPLKIWKSRSCAGISGKSQVLFAVVFTARYLDLLTNYISLYNTYMKVVYIAC

Parental  SYATVYLIYMKFKATYDGNHDTFRVEFLVVPVGGLSFLVNHDFS-PLEILWTFSIYLESVAILPQLFMIS
          S..TV..IY.KFKATYDGNHDTFRVEFLVVP...L.FLVNHDF..PLEILWTFSIYLE.VAILPQLF..S
Retrocopy SFTTVWMIYSKFKATYDGNHDTFRVEFLVVPTAILAFLVNHDFT<PLEILWTFSIYLELVAILPQLFTVS

Parental  KTGEAETITTHYLFFLGLYRALYLVNWIWRFYFEGFFDLIAVVAGVVQTILYCDFFYLYITKVLKGKKLS
          KTG.AETIT.HYLF.LG.YR.LYL.NWIWR..FEGFFDLIA.VAG.VQT.LYCDFFYLYITKVLKGKKLS
Retrocopy KTGKAETITSHYLFALGVYRTLYLCNWIWRYHFEGFFDLIAIVAGLVQTVLYCDFFYLYITKVLKGKKLS

Parental  LPA
          LPA
Retrocopy LPA

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	3.65 RPM	63.42 RPM
SRP017611_brain	2.94 RPM	40.81 RPM
SRP017611_kidney	7.26 RPM	123.36 RPM
SRP017611_liver	5.51 RPM	77.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_318 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_318 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_318 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,