RetrogeneDB ID: retro_cfam_621

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:12134174..12136252(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000001783
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VPS52
• Ensembl ID: ENSCAFG00000000941
• Aliases: None
• Description: Canis lupus familiaris vacuolar protein sorting 52 homolog (S. cerevisiae) (VPS52), mRNA. [Source:RefSeq mRNA;Acc:NM_001048088]

Sequence

>retro_cfam_621
GGGGGTGGCCCTGGTCTTCAGGAGCCATTGCCACTTGGAGAATTGGACATTTCCTCTGATGAATTTATTCTGGATGAAGT
GGATGTTCACATTCAGGCACATCTGGAGGATGAGTTAGTAAAGGAAGCTCTTAAAACGGGTGTGGATCTCCGTCACTATT
CAAAGCAGGTTGAGCTGGAGCTACAGCAGATTGAGCAGAAATCCATTCGAGATTATATCCAGGAGAGTGAGAACATAGCG
TCTCTCCACAACCAGATCACAGCCTGCGATGCTGTTCTTGAGCGCATGGAGCAGATGTTGGGAGCTTTTCAGAGTGACCT
CAGCTCTATTAGCTCTGAGATCCGGACACTGCAGGAACAGTCAGGAGCCATGAATATTCGGCTTCGAAACCGCCAGGCAG
TTCGGGGAAAACTTGGGGAACTTGTCGATGGTCTGATAGTGCCCTCTGCTCTGATCATGGCCATTCTGGAGGCACCAGTG
ACAGAGCCCAGGTTCCTGGAGCAGCTGCAGGAACTGGATGCCAAGGCGGCTGCAGTCCGAGAGCAGGAGGCTAGAGGCAC
AGCGGTTTGTGCTGATGTCAGAGGCATACTTGACGGGCTACGGGTGAAGGCGGTGACGAAGATCCAAGAGTTCATCCTTC
AGAAGATTTATTCCTTCAGAAAACCAATGTCCAACTATCAGATCCCCCAGACGGCCCTGCTCAAGTACAGGTTCTTCTAC
CAGTTTCTGCTGGGCAATGAACGGGCAGTGGCAAAGGAGATCAGGGATGAGTATGTGGAAACGCTGAGCAAGATCTACCT
GTCTTACTATCGCTCTTACCTAGGGCGGCTCATGAAAGTGCAGTATGAGGAAGTTGCCGAGAAGGATGATCTAATGGGTG
TGGAAGACACAGCAAAGAAAGGATTCTTCTCAAAGCCTTCCCTCCGCAGCAGGAACACCATCTTCACCCTGGGGACCCGT
AGGTCTGTCATCTCCCCCACTGAAATGGAGCCCCCCATCCTGGTGCCCCACACTGCCCAGCGGGGAGAACAGAGGTATCC
ATTTGAGGCCCTCTTCTGCAGCCAGCACTACGCCCTCCTAGACAATTCTTGCCGTGAATATCGTTTCATCTGTGAATTCT
TTGTTGTATCCGGCTCGGCTGCACATGATCTCTTCCATGCTGTCATGGGTCGCACCCTTGGCATGACCCTGAAACACCTG
GAGTCCTATCTCACAGACTGCTACGATGCCATTGCTGTTTTACTCTGTATCCACATCGTCCTCTGGTTCCGTAACATTGC
AGTGAAGAGGGATGTTCCTGCCCTGGACAGGTACTGGGAGCAAGCGTTTGCCTTGCTGTGGCCACGGTTTGAGCTGATCC
TGGAGATGAATGTCCAGAGTGTCCGAAGCACTGACCCTCAGCACCTAGGGGGGCTGGATACTTGGCCCCACTATATCACG
CCCGATATGCAGAGTTCTCGTCTGCTCTTGTCAGCATCAATCAGACAGTTCCCAATGAACGGACAATGCAGCTGCCAGGA
CAGCTACAGGTGGAGGTGGAGAATTTTGTCCTCCAAGTGGCAGCTGAGTTCTCCTCAAGGAAGGAGCAACTTGTGCTTTT
GATCAACAACTATGACATGATGCTGGGCATGCTAATGGAGCGGGCTGCAGATGACAGCAAAGAGGTTGAGAGTTTCCAGC
AGCTGCTCAATGCTCGGACACAGGAATTCATTGAAGAGTTGTTGTCTCCCCCTTTTGGGGGTCTGGTGGCATTTGTGAAG
GAAGCCGAGGCTTTAATTGAACGTGGACAGGCTGAGCGACTTCGACGGGAAGAAGCCCAGGTTACTCAACTGATCCGTGG
CTTTGGTAGTTCCTGGAAATCATCAGTGGAGTCTCTGAGTCAGGAGGTAATGCGGGGTTTCACCAACTTCAGAAATGGAA
CCAGTATCATCCAGGGAGCTTTGACCCAGCTGATCCAGCTCTATCATCGCTTCCACCGGGTACTCTCTCAGCCCCAGCTC
CGAGCTCTCCCTGCCCAGGTGGAGCTTATCAACATTCATCACCTTATGGTGGAGCTCAAGAAGCACAAGCCCAACTTT

Alignment

ORF - retro_cfam_621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.95 %
• Parental protein coverage: 95.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGGPGLQEPLPLGELDISSDEFILDEVDVHIQANLEDELVKEALKTGVDLRHYSKQVELELQQIEQKSIR
          GGGPGLQEPLPLGELDISSDEFILDEVDVHIQA.LEDELVKEALKTGVDLRHYSKQVELELQQIEQKSIR
Retrocopy GGGPGLQEPLPLGELDISSDEFILDEVDVHIQAHLEDELVKEALKTGVDLRHYSKQVELELQQIEQKSIR

Parental  DYIQESENIASLHNQITACDAVLERMEQMLGAFQSDLSSISSEIRTLQEQSGAMNIRLRNRQAVRGKLGE
          DYIQESENIASLHNQITACDAVLERMEQMLGAFQSDLSSISSEIRTLQEQSGAMNIRLRNRQAVRGKLGE
Retrocopy DYIQESENIASLHNQITACDAVLERMEQMLGAFQSDLSSISSEIRTLQEQSGAMNIRLRNRQAVRGKLGE

Parental  LVDGLIVPSALIMAILEAPVTEPRFLEQLQELDAKAAAVREQEARGTAACADVRGILDRLRVKAVTKIRE
          LVDGLIVPSALIMAILEAPVTEPRFLEQLQELDAKAAAVREQEARGTA.CADVRGILD.LRVKAVTKI..
Retrocopy LVDGLIVPSALIMAILEAPVTEPRFLEQLQELDAKAAAVREQEARGTAVCADVRGILDGLRVKAVTKIXX

Parental  FILQKIYSFRKPMTNYQIPQTALLKYRFFYQFLLGNERATAKEIRDEYVETLSKIYLSYYRSYLGRLMKV
          ...........PM.NYQIPQTALLKYRFFYQFLLGNERA.AKEIRDEYVETLSKIYLSYYRSYLGRLMKV
Retrocopy XXXXXXXXXXXPMSNYQIPQTALLKYRFFYQFLLGNERAVAKEIRDEYVETLSKIYLSYYRSYLGRLMKV

Parental  QYEEVAEKDDLMGVEDTAKKGFFSKPSLRSRNTIFTLGTRGSVISPTELEAPILVPHTAQRGEQRYPFEA
          QYEEVAEKDDLMGVEDTAKKGFFSKPSLRSRNTIFTLGTR.SVISPTE.E.PILVPHTAQRGEQRYPFEA
Retrocopy QYEEVAEKDDLMGVEDTAKKGFFSKPSLRSRNTIFTLGTRRSVISPTEMEPPILVPHTAQRGEQRYPFEA

Parental  LFRSQHYALLDNSCREYLFICEFFVVSGSAAHDLFHAVMGRTLGMTLKHLESYLTDCYDAIAVFLCIHIV
          LF.SQHYALLDNSCREY.FICEFFVVSGSAAHDLFHAVMGRTLGMTLKHLESYLTDCYDAIAV.LCIHIV
Retrocopy LFCSQHYALLDNSCREYRFICEFFVVSGSAAHDLFHAVMGRTLGMTLKHLESYLTDCYDAIAVLLCIHIV

Parental  LRFRNIAAKRDVPALDRYWEQVLALLWPRFELILEMNVQSVRSTDPQRLGGLDTRPHYIT-RRYAEFSSA
          L.FRNIA.KRDVPALDRYWEQ..ALLWPRFELILEMNVQSVRSTDPQ.LGGLDT.PHYIT..RYAEFSSA
Retrocopy LWFRNIAVKRDVPALDRYWEQAFALLWPRFELILEMNVQSVRSTDPQHLGGLDTWPHYIT<ARYAEFSSA

Parental  LVSINQTVPNERTMQLLGQLQVEVENFVLRVAAEFSSRKEQLVFLINNYDMMLGVLMERAADDSKEVESF
          LVSINQTVPNERTMQL.GQLQVEVENFVL.VAAEFSSRKEQLV.LINNYDMMLG.LMERAADDSKEVESF
Retrocopy LVSINQTVPNERTMQLPGQLQVEVENFVLQVAAEFSSRKEQLVLLINNYDMMLGMLMERAADDSKEVESF

Parental  QQLLNARTQEFIEELLSPPFGGLVAFVKEAEALIERGQAERLRGEEARVTQLIRGFGSSWKSSVESLSQD
          QQLLNARTQEFIEELLSPPFGGLVAFVKEAEALIERGQAERLR.EEA.VTQLIRGFGSSWKSSVESLSQ.
Retrocopy QQLLNARTQEFIEELLSPPFGGLVAFVKEAEALIERGQAERLRREEAQVTQLIRGFGSSWKSSVESLSQE

Parental  VMRSFTNFRNGTSIIQGALTQLIQLYHRFHRVLSQPQLRALPARAELINIHHLMVELKKHKPNF
          VMR.FTNFRNGTSIIQGALTQLIQLYHRFHRVLSQPQLRALPA..ELINIHHLMVELKKHKPNF
Retrocopy VMRGFTNFRNGTSIIQGALTQLIQLYHRFHRVLSQPQLRALPAQVELINIHHLMVELKKHKPNF

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	68.16 RPM
SRP017611_brain	0.08 RPM	73.68 RPM
SRP017611_kidney	0.00 RPM	34.47 RPM
SRP017611_liver	0.00 RPM	22.84 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_621 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_621 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_621 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	ENSCAFG00000000941	1 retrocopy	retro_cfam_621 ,