RetrogeneDB ID: retro_cpor_810

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_29:6541459..6542175(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PMM2
• Ensembl ID: ENSCPOG00000000235
• Aliases: None
• Description: None

Sequence

>retro_cpor_810
CCAGTGCTGTGCCTCTTCCATGTGGATGGGACCCTGATAGCCCTGCAGTAGAAAATTACCAAAGAAGTGGATGACTTTCT
ATAAAAATTGAATCAGAAGACCAAAACTGGAGTGGTAGGCAGGTCAGACTTTGAGAAAATACAGGAACAACTGGGAAATG
ATGTGGTGGAGAAATATGTGTTTCCATAAAATGGCTTGGTAGCATACAAAGATGGAAAAGTCTTATGTAAACAGAATACT
GAAGGTCACCTGGGTGAGGCCCTAATTTAAGATTTAATCAATTACTGTCCAAGCTACACTGCAAAAATTAAACTCCCAAA
GAAAAGGAGTACTTCACTGAATTCTGAAATGGGATGCTGAATGTGTCCCCTATTGGAAGAAGCTGCAGCTAAGGAGAAAG
CATTGAGTTCTACGAACTTGATAAAAAAGAAAACATAAGACAAAATTTCATAGTGGATCTGCAGAAGGAGGTTTCAGGAA
AAGGCCTCACGTTTTCCATAGGAGGCCAAGTCAGCTTTGATGTCTTTTCTGATGGATGGGATAAGAGATGCTGCCTGAGA
CAGGTGGGAAATGATGGTTTTAAGACCATTTACTTCTTTGGAGACAAAACTGTGCCAGGTGACAATGACTATGCGATCTT
CATAGACCCTTGAACAGTGGGCTACACCATGACAACACCCAAAAACAAACGCAGGCTTTGTGAAGAGCTCTTCTCT

Alignment

ORF - retro_cpor_810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.86 %
• Parental protein coverage: 97.97 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVLCLFDVDGTLTAPRQKITKEMDDFLQKLKQKIKIGVVGGSDLEKVQEQLGNDVVQKYNYVFPENGLVA
          PVLCLF.VDGTL.A...KITKE.DDFL.KL.QK.K.GVVG.SD.EK.QEQLGNDVV.KY..VFP.NGLVA
Retrocopy PVLCLFHVDGTLIALQ*KITKEVDDFL*KLNQKTKTGVVGRSDFEKIQEQLGNDVVEKY--VFP*NGLVA

Parental  FKDGKLLCKQSIQGHLGEALIQDLINYCLSYIAKIKLPKKRGT-FIEFRNGMLNVSPVGRSCSQEERIEF
          .KDGK.LCKQ...GHLGEALI.DLINYC.SY.AKIKLPKKR.T.F.EF.NGMLNVSP.GRSCS..E.IEF
Retrocopy YKDGKVLCKQNTEGHLGEALI*DLINYCPSYTAKIKLPKKRST<FTEF*NGMLNVSPIGRSCS*GESIEF

Parental  YELDKKENIRQKFVADLQKEFAGKGLTFSIGGQISFDVFPDGWDKRYCLRHVENDGYKTIYFFGDKTMPG
          YELDKKENIRQ.F..DLQKE..GKGLTFSIGGQ.SFDVF.DGWDKR.CLR.V.NDG.KTIYFFGDKT.PG
Retrocopy YELDKKENIRQNFIVDLQKEVSGKGLTFSIGGQVSFDVFSDGWDKRCCLRQVGNDGFKTIYFFGDKTVPG

Parental  GNDYEIFTDPRTVGYTVTAPEDTRRICEELFA
          .NDY.IF.DP.TVGYT.T.P...RR.CEELF.
Retrocopy DNDYAIFIDP*TVGYTMTTPKNKRRLCEELFS

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	11.39 RPM
SRP017611_kidney	0.00 RPM	15.28 RPM
SRP017611_liver	0.00 RPM	8.62 RPM
SRP040447_lung	0.03 RPM	10.04 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.77 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_810 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_810 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000235	1 retrocopy	retro_cpor_810 ,
Homo sapiens	ENSG00000140650	2 retrocopies	retro_hsap_1869, retro_hsap_1913,
Gorilla gorilla	ENSGGOG00000010124	1 retrocopy	retro_ggor_1399,
Monodelphis domestica	ENSMODG00000005737	1 retrocopy	retro_mdom_285,
Nomascus leucogenys	ENSNLEG00000010062	1 retrocopy	retro_nleu_3062,
Otolemur garnettii	ENSOGAG00000016560	1 retrocopy	retro_ogar_1095,
Pongo abelii	ENSPPYG00000007084	2 retrocopies	retro_pabe_1583, retro_pabe_1584,
Pan troglodytes	ENSPTRG00000007748	2 retrocopies	retro_ptro_1249, retro_ptro_1279,
Sus scrofa	ENSSSCG00000021236	1 retrocopy	retro_sscr_329,