RetrogeneDB ID: retro_cfam_1715

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:81393942..81395611(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000019017
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GPI
• Ensembl ID: ENSCAFG00000007303
• Aliases: None
• Description: Glucose-6-phosphate isomerase [Source:UniProtKB/TrEMBL;Acc:E2R2C3]

Sequence

>retro_cfam_1715
GTGGCCGCGCTCGCCCAGAACCCGCGGTTCCAGAAGCTGCAGAAGAGGCATCCCGAGCCGGGCTCGGACCTCAACCTGCG
CCGCCTTTTCGAGGGGGACAGGGAACGCTTCGACCGCTTCAGCTTGAACCTGAACACCAACCATGGGCGTATTCTGGTGG
ATCACTCCGAGAACCTGGTGACCGACACCGTGATGCAGATGCTGGTGGACCTGGCCAAGTGCAGGGGTGTGGAGGCTGCC
CGGGAGCGCATCAGGGGCGAGAAGATCAACCTCGCGGAGGATCGGGCGGTGCTGCATGTGGCCCTGCGGAACCGGTCAAA
CACACCCGTTCTGGTGGATGGCACGGATGTGATGCCGGAGGGCAACAGGGTCCTGGAGAAGGTGAAGTCTTCCCGCCAGC
GCGTCCGCAGCGGAGAGTGGAAGGGGTACTCGGGCAAGCCCATCACGGGCGTCATTAACATCGGCATTGGCGGCTCTGCG
CTGGGGCCCCTCATGGTGACTGAAGCCCTTAAGCCGTACTCTTCAGGAGGACCCCGGGTCTGGTTTGCCTCCAACACCGA
CGGGACCCACATTTCCAACACCCCGGCCGCCCTGAACCCTGAGTCCTCTCTGGTCATCATTGCCCCCAAGACCTTTACCA
CCCAGGAGACCATTACAAATGCGGAGACGGCGAAGGGAGGGTTTCTCCTGTCGGCCAAGGATCCTTCTGCAGTCGCGAAG
CGCTTTGTCGCCCTGTCTACCAACGCGACCAAAGTGAAGGAGTTTGGGATTGACCCTCAGAACATGTTCGAGTCCCGGGA
TTGGGTGGGAGGACGCTACTCGCTGTGGTCAGCCATTGGACTCTCCATTGCACCGCACGTGGGATTTGACAACGTCGAGC
AGCTGCTCTCAGGGGCTCACTGGATGGACCAGCACTTCCGTACGACGCCCCTGGAGAAGAACGCCCCTGTCCTGCTGGCT
CTGCTGGGCACCTGGTACATCAACTGCTTTGGGTGTGAGACGCAGGCCGTGCTGCCCTACGACCAGTACCTGCACCGCTT
TGCTGCCTACTTCCAGCAGGGTGACATGGGGTCCAACGGGAAGTGCATCACCAAGTCCCGCACTCGTGTGGACACCAGAC
GGGCCCCATCGTGTGGGGGGAGCCAGGGACCAAGGCCAGCACGCCTTCTATCAGCTCATCCACCAAGGCACCAAGATGAT
ACCCTGTGACTTCCGCATCCCGGTCCAGACCCAGCACCCGATAAGGAAGGGTTTGCATCACAAGATCCTCCCGGCCAACT
TTTTGGCCCAAACTGAGGCCCTGATGAAGGGGAAGTCGACAGAGGAGGCCCGGAAGGAGCTGCAGGCCGCAGGAAAGAGT
CCAGAGGACTTAGAGAAGCTGTTGCCGCACAAGGTCTTTGAAGGAAATCGCCCAACAAACTCTATTGTGTTCACCAAGCT
CACGCCATTCATTCTGGGAGCCCTGATCGCCATGTACGAGCACAAGATCTTCGTTCAGGGTGTCATCTGGGACATCAGCA
GCTTTGACCAGTGGGGGGTGGAGCTGGGAAAGCAGCTGGCCAAGAAAATTGAGCCTGAACTTGATGGCAGCAGCCCAGTC
ACCTCTCACGACTCTTCCACGAACGGGCTAATCAACTTCATCAAGCAGGAGCGTGAGGCCAGAAGCCAA

Alignment

ORF - retro_cfam_1715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAALTQSPQFQKLQKWHREQGSDLNLRRLFEGDKERFNRFSLNLNTNHGHILVDYSKNLVTDTVMQMLVD
          .AAL.Q.P.FQKLQK.H.E.GSDLNLRRLFEGD.ERF.RFSLNLNTNHG.ILVD.S.NLVTDTVMQMLVD
Retrocopy VAALAQNPRFQKLQKRHPEPGSDLNLRRLFEGDRERFDRFSLNLNTNHGRILVDHSENLVTDTVMQMLVD

Parental  LAKSRGVEAARERMFSGEKINFTEDRAVLHVALRNRSNTPILVDGKDVMPEVNRVLEKMKSFCQRVRSGE
          LAK.RGVEAARER...GEKIN..EDRAVLHVALRNRSNTP.LVDG.DVMPE.NRVLEK.KS..QRVRSGE
Retrocopy LAKCRGVEAARERI-RGEKINLAEDRAVLHVALRNRSNTPVLVDGTDVMPEGNRVLEKVKSSRQRVRSGE

Parental  WKGYSGKPITDVINIGIGGSDLGPLMVTEALKPYSSGGPRVWFVSNIDGTHISKTLAALNPESSLFIIAS
          WKGYSGKPIT.VINIGIGGS.LGPLMVTEALKPYSSGGPRVWF.SN.DGTHIS.T.AALNPESSL.IIA.
Retrocopy WKGYSGKPITGVINIGIGGSALGPLMVTEALKPYSSGGPRVWFASNTDGTHISNTPAALNPESSLVIIAP

Parental  KTFTTQETITNAETAKEWFLLSAKDPSAVAKHFVALSTNTTKVKEFGIDPQNMFEFWDWVGGRYSLWSAI
          KTFTTQETITNAETAK..FLLSAKDPSAVAK.FVALSTN.TKVKEFGIDPQNMFE..DWVGGRYSLWSAI
Retrocopy KTFTTQETITNAETAKGGFLLSAKDPSAVAKRFVALSTNATKVKEFGIDPQNMFESRDWVGGRYSLWSAI

Parental  GLSIALHVGFDNFEQLLSGAHWMDQHFRTTPLEKNAPVLLALLGIWYINCFGCETQAMLPYDQYLHRFAA
          GLSIA.HVGFDN.EQLLSGAHWMDQHFRTTPLEKNAPVLLALLG.WYINCFGCETQA.LPYDQYLHRFAA
Retrocopy GLSIAPHVGFDNVEQLLSGAHWMDQHFRTTPLEKNAPVLLALLGTWYINCFGCETQAVLPYDQYLHRFAA

Parental  YFQQGDMESNGKYITKSGTRVD-HQTGPIVWGEPGT-NGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRK
          YFQQGDM.SNGK.ITKS.TRVD.HQTGPIVWGEPGT..GQHAFYQLIHQGTKMIPCDF.IPVQTQHPIRK
Retrocopy YFQQGDMGSNGKCITKSRTRVD<HQTGPIVWGEPGT<QGQHAFYQLIHQGTKMIPCDFRIPVQTQHPIRK

Parental  GLHHKILLANFLAQTEALMKGKSTEEARKELQAAGKSPEDLEKLLPHKVFEGNRPTNSIVFTKLTPFILG
          GLHHKIL.ANFLAQTEALMKGKSTEEARKELQAAGKSPEDLEKLLPHKVFEGNRPTNSIVFTKLTPFILG
Retrocopy GLHHKILPANFLAQTEALMKGKSTEEARKELQAAGKSPEDLEKLLPHKVFEGNRPTNSIVFTKLTPFILG

Parental  ALIAMYEHKIFVQGVIWDINSFDQWGVELGKQLAKKIEPELDGSSPVTSHDSSTNGLINFIKQEREARSQ
          ALIAMYEHKIFVQGVIWDI.SFDQWGVELGKQLAKKIEPELDGSSPVTSHDSSTNGLINFIKQEREARSQ
Retrocopy ALIAMYEHKIFVQGVIWDISSFDQWGVELGKQLAKKIEPELDGSSPVTSHDSSTNGLINFIKQEREARSQ

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	6.05 RPM	275.18 RPM
SRP017611_brain	6.83 RPM	376.48 RPM
SRP017611_kidney	5.28 RPM	278.15 RPM
SRP017611_liver	2.39 RPM	137.49 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1715 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1715 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007303	3 retrocopies	retro_cfam_1715 , retro_cfam_1935, retro_cfam_2101,
Cavia porcellus	ENSCPOG00000008562	1 retrocopy	retro_cpor_983,
Macropus eugenii	ENSMEUG00000010190	4 retrocopies	retro_meug_1022, retro_meug_1281, retro_meug_559, retro_meug_991,
Microcebus murinus	ENSMICG00000011620	1 retrocopy	retro_mmur_1496,
Myotis lucifugus	ENSMLUG00000003037	1 retrocopy	retro_mluc_444,
Macaca mulatta	ENSMMUG00000005880	1 retrocopy	retro_mmul_2086,
Mustela putorius furo	ENSMPUG00000007520	1 retrocopy	retro_mputfur_1370,
Mus musculus	ENSMUSG00000036427	1 retrocopy	retro_mmus_237,