RetrogeneDB ID: retro_cpor_983

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_38:12805036..12806110(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPI
• Ensembl ID: ENSCPOG00000008562
• Aliases: None
• Description: Glucose-6-phosphate isomerase [Source:UniProtKB/TrEMBL;Acc:H0VCM3]

Sequence

>retro_cpor_983
CATATCTTGTTGGAATAATCCAAGAACCTTGTGATGGAGGAGGGTCTTAAAAGATGGCTGGTGGAACCCAGCCAACTCCC
AGGGATGTGAAGGTTGCCCAGGAGCACATTTCAATGCGAGAAGGTCAACTAGGCCGAGAATGGCACAGTATTGCATATGG
CCCTGAGAAAATCAGTCAAATACACCCATGCTGGTGGATGACAAGATTGTGACACCAAAGATCAACAGAGTTCTGGACAA
GATGAAGTATTTCTGTCAGCATGTCCAGAGTGGCAACTGGAAGGGAGACACAGGCAAAGCCATCACAGATGTCATCGACA
TCTGTTTTGGAGGCTCTGACCTGGAACCTCTCATGGTGACAGAAGCCCGTAAGCCATACTCTTCAGGAGGTCCCCAGGTA
TGGCTTGTCTCCAACACTAATGGGACCCACATTGCCAAGACCCTGGCCAACCTGAGCCCCAAGACATCCCTGTTTATCAT
CACCTCCAAGACCTTTACCCCACAGGAGACCATCACCAATGCAGAGATGGCAAAGGTGTGGTTTCTCATGTCTGCCAAGG
ATGCTTCTGCAGTGGCAAAGCACTTTGTTCTCCTCTCTACCAACACAGCCAAGGTGAAGGAGTTTGGAGCTGACCCTCAA
AACATGTTGGAGTTCTGGACTTGGTAGGTGGATGCTTCTCCCTGTGGCCAGCCATCAGACTCTCCATCAGGCTGCATGTA
GGTTTTGACAACTTTGAGCAGCTGCTCTCCAGAGCTCACTGGATGGACCAGCACTTCCAAATGGGGCCCCTAGAAAAGAA
CACCCCTGTCCTCCTGGCACTGCTGAGGGTCTGGTACATCAACAGCTTTGGGAGTGAGACACAGGTCTTGCCACCCTGTG
ACCAGTACCTGTACTGTTTTCCTGTTTACTTCCAGCAGTGTGACATAAAGTCCAGTGGGAAGTACATCATCAAGGTAGGT
GTCCATTTGGACCACCAGATTGCCCCTAGCATGTGGGGAGAGCCAGGAACCAGTGGTTAGCACACATTCCACCAGCTCAT
CCACCAAGGCACCAAGATGATACCCTTTGACTTC

Alignment

ORF - retro_cpor_983 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 63.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HILLDYSKNLVTEDVMKM-LVELAKSRGVEAARERMFSGEKINYTEDRAVLHVALR-NRSNTPMLVDGKD
          HILL..SKNLV.E...K..LVE.....G........F..EK.N..E...VLH.ALR.N.SNTPMLVD.K.
Retrocopy HILLE*SKNLVMEEGLKRWLVEPSQLPGM*RLPRSTFQCEKVN*AENGTVLHMALR>NQSNTPMLVDDKI

Parental  VMPEINKVLDKMKSFCQRVRNGDWKGYTGKAITDVINIGIGGSDLGPLMVTEALKPYSSGGPHVWFVSNI
          V.P.IN.VLDKMK.FCQ.V..G.WKG.TGKAITDVI.I..GGSDL.PLMVTEA.KPYSSGGP.VW.VSN.
Retrocopy VTPKINRVLDKMKYFCQHVQSGNWKGDTGKAITDVIDICFGGSDLEPLMVTEARKPYSSGGPQVWLVSNT

Parental  DGTHIAKTLANLNPETSLFIIASKTFTTQETITNAETAKEWFLMSAKDASAVAKHFVALSTNTAKVKEFG
          .GTHIAKTLANL.P.TSLFII.SKTFT.QETITNAE.AK.WFLMSAKDASAVAKHFV.LSTNTAKVKEFG
Retrocopy NGTHIAKTLANLSPKTSLFIITSKTFTPQETITNAEMAKVWFLMSAKDASAVAKHFVLLSTNTAKVKEFG

Parental  IDPQNMFEFWDW-VGGRYSLWSAIGLSIALHVGFDNFEQLLSGAHWMDQHFRTAPLEKNAPVLLALLGIW
          .DPQNM.EFW.W.VGG..SLW.AI.LSI.LHVGFDNFEQLLS.AHWMDQHF...PLEKN.PVLLALL..W
Retrocopy ADPQNMLEFWTW<VGGCFSLWPAIRLSIRLHVGFDNFEQLLSRAHWMDQHFQMGPLEKNTPVLLALLRVW

Parental  YINCFGCETQALLPYDQYLHRFPAYFQQGDMESNGKYITKPGVRVDHQTGPIVWGEPGTNGQHAFYQLIH
          YIN.FG.ETQ.L.P.DQYL..FP.YFQQ.D..S.GKYI.K.GV..DHQ..P..WGEPGT.G.H.F.QLIH
Retrocopy YINSFGSETQVLPPCDQYLYCFPVYFQQCDIKSSGKYIIKVGVHLDHQIAPSMWGEPGTSG*HTFHQLIH

Parental  QGTKMIPCDF
          QGTKMIP.DF
Retrocopy QGTKMIPFDF

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
SRP017611_brain	0.00 RPM	475.49 RPM
SRP017611_kidney	0.00 RPM	237.33 RPM
SRP017611_liver	0.13 RPM	94.58 RPM
SRP040447_lung	0.03 RPM	145.37 RPM
SRP040447_skeletal_muscle	0.01 RPM	715.87 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_983 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_983 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,