RetrogeneDB ID: retro_cfam_2101

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:78990143..78991042(+)
• Located in intron of: None

Retrocopy information

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

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_2101
ATGGCCGCGCTCACCCAGAACCCGCAGTGCCAGAAACTGCAGAAGTGGCATCGCTAGCAGGGCTCTGACCTCAACCTGCG
CCACCTTTCGAGGGGGACAAGGAACGCTTCAACTGCTTCAGCTTGAACCTGAACACCAACCATGGGCATATTCTGGTGGA
TTATTCCAAGAACCTTGTGACCGACACTGTGATGCAGATGCTGGTGGACCTGGCCAAGTCCAGGGGTGTGGAGGCTGCCC
AGGAGCGCATGTTCAAAGGCGAGAAGATCAACTTCATGGAGGATCGGGCGGTGCTGCATGTGGCCTTGCGCAACCGGTCA
AACACACCCATTCTGGTGGATGGCAAGGATGTGATGCCAGAGGTCAACAAGGTCCTGGAGAAGATGAAGTCTTTCTGCCA
GCACGTCTGCAATGGTAAGTGGAAGGGGTACTTGGGCAAGCCTATCACGGACGTCATTAACTTCGGCCTTGGCGGCTCTG
ACCTGGGGCTCCTTAGGGTGACTGAAGCCCTTAAGCCGTACTCTTCAGGAGGACCCCGGGTCTGGTTTGTCTCCAACATC
GACGGGACCCACATTTCCAAAACCCTGACCACCCTGAACCCTGAGTCCTCTCTGTTCATCATTGCCTCCAAGACCTTTAC
CACCCAGGAGACCATTACAAATGTGGAGACGGTGAAGGAGTGGTTTCTCCTGTAGGCCAAGGATCCTTCTGCAGTCGCGA
AGCGCTTTGTCGCCCTGTCTACTAACACGACCAAAGTGAAGGAGTTTGGGATTGACCCTCAAAACATGTTGGAGTTCTGG
GATTGGGTGGGAGGATGCTACTCGCTGTGGTCAGCCATTGGACTCTCCATTGCACTGCAAGTGGGATTTGACAACTTCGA
GCAGCTGCTCTCGGGCTCA

Alignment

ORF - retro_cfam_2101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.37 %
• Parental protein coverage: 53.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAALTQSPQFQKLQKWHREQGSDLNLRRL-FEGDKERFNRFSLNLNTNHGHILVDYSKNLVTDTVMQMLV
          MAALTQ.PQ.QKLQKWHR.QGSDLNLR.L.FEGDKERFN.FSLNLNTNHGHILVDYSKNLVTDTVMQMLV
Retrocopy MAALTQNPQCQKLQKWHR*QGSDLNLRHL<FEGDKERFNCFSLNLNTNHGHILVDYSKNLVTDTVMQMLV

Parental  DLAKSRGVEAARERMFSGEKINFTEDRAVLHVALRNRSNTPILVDGKDVMPEVNRVLEKMKSFCQRVRSG
          DLAKSRGVEAA.ERMF.GEKINF.EDRAVLHVALRNRSNTPILVDGKDVMPEVN.VLEKMKSFCQ.V..G
Retrocopy DLAKSRGVEAAQERMFKGEKINFMEDRAVLHVALRNRSNTPILVDGKDVMPEVNKVLEKMKSFCQHVCNG

Parental  EWKGYSGKPITDVINIGIGGSDLGPLMVTEALKPYSSGGPRVWFVSNIDGTHISKTLAALNPESSLFIIA
          .WKGY.GKPITDVIN.G.GGSDLG.L.VTEALKPYSSGGPRVWFVSNIDGTHISKTL..LNPESSLFIIA
Retrocopy KWKGYLGKPITDVINFGLGGSDLGLLRVTEALKPYSSGGPRVWFVSNIDGTHISKTLTTLNPESSLFIIA

Parental  SKTFTTQETITNAETAKEWFLLSAKDPSAVAKHFVALSTNTTKVKEFGIDPQNMFEFWDWVGGRYSLWSA
          SKTFTTQETITN.ET.KEWFLL.AKDPSAVAK.FVALSTNTTKVKEFGIDPQNM.EFWDWVGG.YSLWSA
Retrocopy SKTFTTQETITNVETVKEWFLL*AKDPSAVAKRFVALSTNTTKVKEFGIDPQNMLEFWDWVGGCYSLWSA

Parental  IGLSIALHVGFDNFEQLLSGA
          IGLSIAL.VGFDNFEQLLSG.
Retrocopy IGLSIALQVGFDNFEQLLSGS

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	0.55 RPM	275.18 RPM
SRP017611_brain	0.16 RPM	376.48 RPM
SRP017611_kidney	0.13 RPM	278.15 RPM
SRP017611_liver	0.00 RPM	137.49 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2101 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2101 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,