RetrogeneDB ID: retro_cpor_539

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_187:614355..614805(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM1
• Ensembl ID: ENSCPOG00000006844
• Aliases: None
• Description: phosphoglycerate mutase 1 (brain) [Source:HGNC Symbol;Acc:8888]

Sequence

>retro_cpor_539
AGCGACTGGTACAATCCCAACCTGAGCCCAGCAGGCCACAAAGAGGCAAAGCGTGGCAGGCATGCAATGCAAGATGCTGA
CTATGAATTTGACATCTACTTCACCTTAGTGCAGAAAAGAGTAGTCCAGACCCTCTGGACAGTACTGGATGCCATTGACT
AGATGTGGGTGCCCATGGTAAGAACTCGGCACCTCGAGGAGCAGCACTTTGAGGGTCTGACTGAACTTAATAAAGCAGAA
ACTGCTGCTAAGCACAGTGAGGCTCAGGTGAAGGACTGTAGGTGCTCCTGTGATGCCCCACCACCTCCAACAGAGCCTGA
GCATCCCTTCTACAGCAACATCAGCAAGGATCATAGGTGTGCAGACCTTACTGAAGACCAGATGCCTTCCTGTGAGAGTC
TGAAAGACACTATTGCCAGAGCTCTGTCCTTCTGGAATGAAGAAATTGTT

Alignment

ORF - retro_cpor_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76. %
• Parental protein coverage: 59.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGWYDADLSPAGHEEAKRGGQALRDAGYEFDICFTSVQKRAIRTLWTVLDAIDQMWVPVVRTWRLNERHY
          S.WY...LSPAGH.EAKRG..A..DA.YEFDI.FT.VQKR...TLWTVLDAID.MWVP.VRT..L.E.H.
Retrocopy SDWYNPNLSPAGHKEAKRGRHAMQDADYEFDIYFTLVQKRVVQTLWTVLDAID*MWVPMVRTRHLEEQHF

Parental  GGLTGLNKAETAAKHGEAQVKIWRRSYDVPPPPMEPDHPFYSNISKDRRYADLTEDQLPSCESLKDTIAR
          .GLT.LNKAETAAKH.EAQVK..R.S.D.PPPP.EP.HPFYSNISKD.R.ADLTEDQ.PSCESLKDTIAR
Retrocopy EGLTELNKAETAAKHSEAQVKDCRCSCDAPPPPTEPEHPFYSNISKDHRCADLTEDQMPSCESLKDTIAR

Parental  ALPFWNEEIV
          AL.FWNEEIV
Retrocopy ALSFWNEEIV

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	0.06 RPM	146.38 RPM
SRP017611_kidney	0.00 RPM	102.38 RPM
SRP017611_liver	0.04 RPM	37.13 RPM
SRP040447_lung	0.00 RPM	63.00 RPM
SRP040447_skeletal_muscle	1.25 RPM	37.77 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_539 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_539 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 20 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Cavia porcellus	ENSCPOG00000006844	4 retrocopies	retro_cpor_158, retro_cpor_539 , retro_cpor_605, retro_cpor_660,
Erinaceus europaeus	ENSEEUG00000005630	1 retrocopy	retro_eeur_680,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Loxodonta africana	ENSLAFG00000015979	1 retrocopy	retro_lafr_886,
Microcebus murinus	ENSMICG00000007657	1 retrocopy	retro_mmur_135,
Myotis lucifugus	ENSMLUG00000009117	6 retrocopies	retro_mluc_1280, retro_mluc_1595, retro_mluc_1741, retro_mluc_2246, retro_mluc_632, retro_mluc_745,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Mustela putorius furo	ENSMPUG00000017045	1 retrocopy	retro_mputfur_1409,
Mus musculus	ENSMUSG00000011752	6 retrocopies	retro_mmus_1741, retro_mmus_2221, retro_mmus_3012, retro_mmus_411, retro_mmus_729, retro_mmus_769,
Oryctolagus cuniculus	ENSOCUG00000005679	5 retrocopies	retro_ocun_1016, retro_ocun_1081, retro_ocun_350, retro_ocun_706, retro_ocun_976,
Pan troglodytes	ENSPTRG00000002807	12 retrocopies	retro_ptro_1082, retro_ptro_1580, retro_ptro_1645, retro_ptro_1755, retro_ptro_2080, retro_ptro_2361, retro_ptro_2889, retro_ptro_2890, retro_ptro_3114, retro_ptro_3238, retro_ptro_634, retro_ptro_714,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Sarcophilus harrisii	ENSSHAG00000018230	1 retrocopy	retro_shar_323,
Sus scrofa	ENSSSCG00000010517	1 retrocopy	retro_sscr_373,
Ictidomys tridecemlineatus	ENSSTOG00000025955	1 retrocopy	retro_itri_1187,
Tupaia belangeri	ENSTBEG00000005913	5 retrocopies	retro_tbel_1677, retro_tbel_1708, retro_tbel_2756, retro_tbel_3667, retro_tbel_563,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,