RetrogeneDB ID: retro_cfam_1133

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 24:19499891..19500875(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS26A
• Ensembl ID: ENSCAFG00000013827
• Aliases: None
• Description: vacuolar protein sorting 26 homolog A (S. pombe) [Source:HGNC Symbol;Acc:12711]

Sequence

>retro_cfam_1133
AGGAGTTTTTTTGGAGGCTTTTTTGGACCCATTTGTGAGATCGATGTTGTCCTTAATGATGGGGAAACCAGGAAAATGGC
TGAAATGAAAACTGAAGATGGCAAAGTAGAAAAGTACTATCTTTTCTATGATGGAGAGTTTGTTTCAGAAAAGGTAAACC
TAGCTTTTAAGCAACCTGGAATGAGGCTAGAGCACCAAGGAATTAGAACTGAATTTGTAGATCAAATTGAACTTTTCAAT
GACAGGAATAATACTCATGAGTTTGTAGACCTAGTGAAAGAACTAGCCTTGCCTGGAAAATTGACTCAGAGTAGAAGCTA
TGATTTTGAATTTATGCGATTTGAAAAACTATATGAATCTTATATCAATGCCAATGTCCCCTTGAGGTATTTTCTTAAAG
TGACAATAGTAAGAAGACTGATAAACTTGGTAAAAGGATATGATCTTATTGTTCACCAACTTGCCACATATCCTGATGTT
AACAACTCTATTAAGATGAAAGTGGGCATTGAAAATAGTCTACAAGTATAATTTGAATATAATAAATCAAAATATCATCT
AAGGGATTTGATTGTTGGAAAAATTTACTTCTTATTAGTAAGAATAAAGATCCAACATATGGAGTTGCAACTGGTAAAAA
AAAAAAGGATCACAGGAATTGGACCCAGTACCACCACAGAAACAGAAATAATTGCAAAATATAAAATAATGAATGGTGTA
CCCATAAAAGGTGAATCAATTTCAATAAGACTATTTTTAGTGGGATATGACCCAACTCTGACAATGAGAGATGTGAACAA
AAAATTTTCTGTAAGGTACTTTTTGATTCTAGTCCTTGTTGATGAGGAAGACAGAAGGTACTTCAAGCAGCAGGAGATCA
TCTTATGGAGAAATGCTTCTGAAAAACTGAGGAAACAGAGAACAAACCTTCACCAGCGATTTGAATCATCAGAATTAGAG
GCATCTGCTGAACAGCCTAAAATG

Alignment

ORF - retro_cfam_1133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.76 %
• Parental protein coverage: 96.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSFLGGFFGPICEIDVVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRI
          .SF.GGFFGPICEIDVVLNDGETRKMAEMKTEDGKVEK.YLFYDGE.VS.KVNLAFKQPG.RLEHQGIR.
Retrocopy RSFFGGFFGPICEIDVVLNDGETRKMAEMKTEDGKVEKYYLFYDGEFVSEKVNLAFKQPGMRLEHQGIRT

Parental  EFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRL
          EFV.QIELFND..NTHEFV.LVKELALPG.LTQSRSYDFEFM..EK.YESYI.ANV.LRYFLKVTIVRRL
Retrocopy EFVDQIELFNDRNNTHEFVDLVKELALPGKLTQSRSYDFEFMRFEKLYESYINANVPLRYFLKVTIVRRL

Parental  TDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQ
          ..LVK.YDLIVHQLATYPDVNNSIKM.VGIE..L...FEYNKSKYHL.D.IVGKIYFLLVRIKIQHMELQ
Retrocopy INLVKGYDLIVHQLATYPDVNNSIKMKVGIENSLQV*FEYNKSKYHLRDLIVGKIYFLLVRIKIQHMELQ

Parental  L-IKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLV
          L.....ITGIGPSTTTETE.IAKY.IM.G.P.KGESI.IRLFL.GYDPT.TMRDVNKKFSVRYFL.LVLV
Retrocopy LXXXXXITGIGPSTTTETEIIAKYKIMNGVPIKGESISIRLFLVGYDPTLTMRDVNKKFSVRYFLILVLV

Parental  DEEDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASPEQPEM
          DEEDRRYFKQQEIILWR.A.EKLRKQRTN.HQRFES.E..AS.EQP.M
Retrocopy DEEDRRYFKQQEIILWRNASEKLRKQRTNLHQRFESSELEASAEQPKM

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	0.04 RPM	42.84 RPM
SRP017611_brain	0.00 RPM	41.20 RPM
SRP017611_kidney	0.00 RPM	90.21 RPM
SRP017611_liver	0.00 RPM	21.90 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1133 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1133 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013827	1 retrocopy	retro_cfam_1133 ,
Choloepus hoffmanni	ENSCHOG00000007324	5 retrocopies	retro_chof_1303, retro_chof_1663, retro_chof_1796, retro_chof_2352, retro_chof_242,
Callithrix jacchus	ENSCJAG00000012907	1 retrocopy	retro_cjac_1420,
Equus caballus	ENSECAG00000009507	1 retrocopy	retro_ecab_17,
Homo sapiens	ENSG00000122958	1 retrocopy	retro_hsap_2688,
Gorilla gorilla	ENSGGOG00000010433	1 retrocopy	retro_ggor_1875,
Microcebus murinus	ENSMICG00000014940	1 retrocopy	retro_mmur_1070,
Mustela putorius furo	ENSMPUG00000004519	1 retrocopy	retro_mputfur_146,
Nomascus leucogenys	ENSNLEG00000011548	1 retrocopy	retro_nleu_1187,
Pongo abelii	ENSPPYG00000002386	1 retrocopy	retro_pabe_2293,
Pan troglodytes	ENSPTRG00000002567	3 retrocopies	retro_ptro_1815, retro_ptro_2245, retro_ptro_4,
Tupaia belangeri	ENSTBEG00000015348	1 retrocopy	retro_tbel_1425,
Vicugna pacos	ENSVPAG00000000630	1 retrocopy	retro_vpac_385,