RetrogeneDB ID: retro_ggor_464

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:184552627..184553467(-)
• Located in intron of: ENSGGOG00000012957

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEF1
• Ensembl ID: ENSGGOG00000015897
• Aliases: None
• Description: None

Sequence

>retro_ggor_464
GCCAGCTATCTGTATGGGCAGGGCTGCCCTGGAGATGCAGGGCAAGCGCCAGGAACCCCTCCGGGTAGCTACTACCTTGG
ACCCCCCCAATAGTGGAGGGCAGTATGGCAGCGTGCTACCCCCTGGTGGTGGCTATGGGGGTCCTGCCCCTGGAGGGCCT
TATGGACCACCAGCTGGTAGAGGGCCCTATGGACACCTCAATCCTGGGATGTTCCCCTCTGGAACTCCAGGAGGACCAAA
TGATGGTACAGCTCCAGGGGGCCCCTATGGTCAGCCACCTCCAAATTCCTACGGTGCCCAGCAGCCCAGGCCTCATGGAC
AGGGTGGCTCCCCTCCCAATATGGATGAGGCCTACTCCTGGTTCCAGTCGGTGACTCCGATCACAGTGGCTTTATCTCCA
TGAAGGAGGTGAAGCAGGCTCTGGTCAACTGCAACTGGTCCTTGTTCAATGAGACCTGCCTCATGATGATAAACATGTTT
GACAAGACCTAATCAGGCCACATCAATGTCTACGGCTTCTCAGCCCTGTGGAAATTCATCCAGCAGTGGAAGCAGCTCTT
CCAGCAGTTATGACTGGGACAACTCAGGCTCCATTAGCTACACAGAGCTGCAGCAAGCTCTATCCCAAAAGGGCTACAAC
CTGAGCCCCCAGTTCACCCAGCTACTGGTCTCCAGCTACTGCCCACGACTGTCAATCCTGCCAGACAGCTTGATTGCTTC
ACCCAGGTGTGCACCCAGCTGCAGATGCCGACAGAGGCCTTCCGGGAGAAGGACACAGCTGTACAAGGCAACATTCGGCT
CAGCTTCAAGGACGTCGTCACCATGACAGCTCGGATGCTA

Alignment

ORF - retro_ggor_464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.32 %
• Parental protein coverage: 99.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ASYPYRQGCPGVAGQAPGAPPGSYYPGPP-SSGGQYGSGLPPGGGYGGPAPGGPYGPPAGGGPYGHPNPG
          ASY.Y.QGCPG.AGQAPG.PPGSYY.GPP..SGGQYGS.LPPGGGYGGPAPGGPYGPPAG.GPYGH.NPG
Retrocopy ASYLYGQGCPGDAGQAPGTPPGSYYLGPP>NSGGQYGSVLPPGGGYGGPAPGGPYGPPAGRGPYGHLNPG

Parental  MFPSGTPGGPYGGAAPGGPYGQPPPSSYGAQQPGLYGQGGAPPNVDPEAYSWFQSV-DSDHSGYISMKEL
          MFPSGTPGGP..G.APGGPYGQPPP.SYGAQQP...GQGG.PPN.D.EAYSWFQSV.DSDHSG.ISMKE.
Retrocopy MFPSGTPGGPNDGTAPGGPYGQPPPNSYGAQQPRPHGQGGSPPNMD-EAYSWFQSV<DSDHSGFISMKEV

Parental  KQALVNCNWSSFNDETCLMMINMFDKTKSGRIDVYGFSALWKFIQQWKNLFQQ-YDRDRSGSISYTELQQ
          KQALVNCNWS.FN.ETCLMMINMFDKT.SG.I.VYGFSALWKFIQQWK.LFQQ.YD.D.SGSISYTELQQ
Retrocopy KQALVNCNWSLFN-ETCLMMINMFDKT*SGHINVYGFSALWKFIQQWKQLFQQ>YDWDNSGSISYTELQQ

Parental  ALSQMGYNLSPQFTQLLVSRYCPR-SANPAMQLDRFIQVCTQLQVLTEAFREKDTAVQGNIRLSFEDFVT
          ALSQ.GYNLSPQFTQLLVS.YCPR...NPA.QLD.F.QVCTQLQ..TEAFREKDTAVQGNIRLSF.D.VT
Retrocopy ALSQKGYNLSPQFTQLLVSSYCPR<TVNPARQLDCFTQVCTQLQMPTEAFREKDTAVQGNIRLSFKDVVT

Parental  MTASRML
          MTA.RML
Retrocopy MTA-RML

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
SRP007412_brain_prefrontal_cortex	0.19 RPM	43.25 RPM
SRP007412_cerebellum	0.04 RPM	42.27 RPM
SRP007412_heart	0.03 RPM	22.55 RPM
SRP007412_kidney	0.00 RPM	42.12 RPM
SRP007412_liver	0.00 RPM	39.22 RPM
SRP007412_testis	0.00 RPM	34.71 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_464 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_497
Pan troglodytes	retro_ptro_375
Pongo abelii	retro_pabe_238

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006355	1 retrocopy	retro_cjac_1745,
Homo sapiens	ENSG00000162517	1 retrocopy	retro_hsap_497,
Gorilla gorilla	ENSGGOG00000015897	1 retrocopy	retro_ggor_464 ,
Macropus eugenii	ENSMEUG00000014458	1 retrocopy	retro_meug_375,
Microcebus murinus	ENSMICG00000001374	1 retrocopy	retro_mmur_937,
Macaca mulatta	ENSMMUG00000023397	1 retrocopy	retro_mmul_146,
Monodelphis domestica	ENSMODG00000017573	1 retrocopy	retro_mdom_1930,
Nomascus leucogenys	ENSNLEG00000001979	1 retrocopy	retro_nleu_2422,
Oryctolagus cuniculus	ENSOCUG00000005744	1 retrocopy	retro_ocun_461,
Pongo abelii	ENSPPYG00000001611	1 retrocopy	retro_pabe_238,
Pan troglodytes	ENSPTRG00000000463	1 retrocopy	retro_ptro_375,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563, retro_rnor_2505,