RetrogeneDB ID: retro_cfam_1407

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:24751611..24752597(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000002325
• Aliases: None
• Description: Glyceraldehyde-3-phosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:E2RNN4]

Sequence

>retro_cfam_1407
ATGGTGAAGGTCGGAGTGAACGGATTTGGCCGTATTGGGCGCCTGGTCACCAGGGCTGCTTTTAATTCTGGCAAAATGGA
TATTGTCGCCATCAATGACCCCTTCATTGACCTCAACCTCATGGTATACATGTTCCAGTATGATTCTACCCATGGCAAAT
TCCACAGCACAGTCAAGGCTGAGAATGGGAAACTTGTCATCAATGGGAAGTCCATCTCTATCTTCCAGGAGCGAGATCCT
GCCAACATCAAATGGGGTAATGCTGGTGCTGAGTATGTTGTGGAGTCCACTGGGGTCTTCACCACCATGGAGAAGGCTGG
GGCTCACTTGAAGGGTGGGGCCAAGAGGGTCATCATCTCTGCTCCTTCTGCTGATGCCCCCATGTTTGTGATGGGCGTGA
ACCACAAGAAGTATGACAACTCCCTCAAGATTGTCACAATGCTTCCTGCACCATCAATTGCTTGGCTTCTCTGGCCAAAG
TCATCCATGACCACTTTGGCATCATGGAGGGCCTCATGATCACTGTCCATGCCATCACTGCCACCCAGAAGACCGTGGAC
GGCCCCTCTGGGAAGCTGTGGCATGATGGCTGAGGGGATGCCCAGAACATCATCCCTGCTTTCACTGGCACTGCTAAGGC
TATGGGCAAGGTCATCCTTGAAGCTCACTGTATGGCCTTCCGTGTCCCCACCCCCAACATGTCAGTTGTGGATCTGACCG
GCCGCCTGGAGAAAGCTGCCAAATATGACAACATCAAGAAGGTGGTGAAGCAGGCATCAGAGGGCCCCCTCAAGGGCATC
CTGGGCTACACTGAGGACCAGGTTGTCTCCTGCAACTTCAACAGTGACACTCACTCTTCCACCTTTGACACCAAGGCTGG
CATTGCCCTCAATGACCACTTCGTCAAGCTCATTTCCTGGTATGACAATGAATTTGGCTACAGCAACTAGGTGGTGGACC
TCATGGTCCACATGGCCTCCAAGGAG

Alignment

ORF - retro_cfam_1407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVKLGVNEFAHIGRLGTRAAFNSGKEDIVTINDSFIDLNYMVYMFQYDSTHGKFYGMVKAENGKLVINGK
          MVK.GVN.F..IGRL.TRAAFNSGK.DIV.IND.FIDLN.MVYMFQYDSTHGKF...VKAENGKLVINGK
Retrocopy MVKVGVNGFGRIGRLVTRAAFNSGKMDIVAINDPFIDLNLMVYMFQYDSTHGKFHSTVKAENGKLVINGK

Parental  SISIFQERHPANNKWGDAGAEYVVEPTGVFTTMENAGAHLKSGAKRVIISAPSADAPMFVMGVNHEKYNK
          SISIFQER.PAN.KWG.AGAEYVVE.TGVFTTME.AGAHLK.GAKRVIISAPSADAPMFVMGVNH.KY..
Retrocopy SISIFQERDPANIKWGNAGAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAPSADAPMFVMGVNHKKYDN

Parental  SLKIVS-NASCTTNCLAPLAKVIHDHFGIVEGLMTTAHAITATQKTMGGTSGKLWPEGRVPVQNIIPAST
          SLKIV..NASCT.NCLA.LAKVIHDHFGI.EGLM.T.HAITATQKT..G.SGKLW..G....QNIIP...
Retrocopy SLKIVT<NASCTINCLASLAKVIHDHFGIMEGLMITVHAITATQKTVDGPSGKLWHDG*GDAQNIIP---

Parental  GAATAVGKVIPELKGKFIGMAFRVPTPNMSVVDLTCPLEKAAKYDNIKKVVKQASEGPLKGIL--AEDQV
          .A.T...K...........MAFRVPTPNMSVVDLT..LEKAAKYDNIKKVVKQASEGPLKGIL...EDQV
Retrocopy -AFTGTAKAMGKVILEAHCMAFRVPTPNMSVVDLTGRLEKAAKYDNIKKVVKQASEGPLKGILGYTEDQV

Parental  VSCDFNSDTHPSIFDTGAGIAFNDHLVKHSSVKYSINKFSFSSSEVEISSHIIHED
          VSC.FNSDTH.S.FDT.AGIA.NDH.VK........N.F..S...V....H.....
Retrocopy VSCNFNSDTHSSTFDTKAGIALNDHFVK--LISWYDNEFGYSN*VVDLMVHMASKE

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	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.07 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1407 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1407 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1407 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002325	1 retrocopy	retro_cfam_1407 ,
Canis familiaris	ENSCAFG00000015077	4 retrocopies	retro_cfam_122, retro_cfam_214, retro_cfam_3, retro_cfam_7,
Tupaia belangeri	ENSTBEG00000001510	27 retrocopies	retro_tbel_1055, retro_tbel_1149, retro_tbel_1315, retro_tbel_1359, retro_tbel_1519, retro_tbel_1684, retro_tbel_232, retro_tbel_2380, retro_tbel_2442, retro_tbel_2731, retro_tbel_2992, retro_tbel_3109, retro_tbel_3205, retro_tbel_3418, retro_tbel_3463, retro_tbel_3826, retro_tbel_3829, retro_tbel_393, retro_tbel_4036, retro_tbel_4094, retro_tbel_4310, retro_tbel_4377, retro_tbel_441, retro_tbel_4560, retro_tbel_4635, retro_tbel_4706, retro_tbel_480,