RetrogeneDB ID: retro_ggor_1346

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:43375079..43376038(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000023473
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ASS1
• Ensembl ID: ENSGGOG00000010228
• Aliases: None
• Description: None

Sequence

>retro_ggor_1346
CTCGCCAGGCCCTGCATCGCCTGCAAACAAATGGAAATCACCCAGTGGAAGGGGGCCAAGTATATGTCCCACAGCGCCAC
GGGAAATGGGAACAATCAGGTCCGGTTTGAGCTCATTTGCTACTCGCTGGCACCCCAGATAAAGGTCATTGCTCCCTGGA
GGATGCCCAAATTCTACAACCAGCTCAAGGGCCGCAATGACCTGATGGAATATGCAAAGCAACACAGGATTCCCATCCCG
GTCACACCCAAGAACTCATGGAGCAGGGACGAGAACCTCATGCATATCAGCTACGAGGCTGGAATCCCGGAGAACCCTAA
GAACCAAGCACCTCCAGGTCTCTACACGAAGACCAGGACCCGGCCAAAGCCCCCAACACCCCTGACATTCTCAAGATCGA
GTTCAAAAAAGGAGTCCCCGTGAAGGTGACCAACGTCAAGGATGGCACCACCCACCAGACCTCCTTGGAGCTCTTCATGT
ACCTGAACGAAGTCGTGGGCAAGCAGGGTGTGGGCTGTATTGACATCATGGAGAACCGCTTCATTGGAATGAAGTCCCGA
GGTATCTACCAGGCCCCAGCAAGCACCATCCTTTACCTCGCTCATTTAGACACCAAGGCCTTCACCATGGACCAGGAAGT
GCACAAAATCAAACAAGGCCTGGGCTTGAAATTTGTTGAGCTGGTGGATACCAGTTTCTGGTACAGCCCTGAGTGTGAAT
TTGTCTGCCACTGCATCGCCAAGTCCCAGGAGCAAGTGGAAGGGAAAGTGCAGGTGTCCGTCCTCGAGGGCCAGGTGTAC
ATCCTTGGCCAGGAGTCCCCACTGTCTCTCTACAAGGAGGAGCCGGTGAGCATGAACGTGCAGGGTGATTATCAGCCAAT
TGATGCCACCGGGTTCATCAACATCAGTTCCCTCAGGCTGAAGGAATATCATCGTCTCCAGAGCAAGGTCACTGCCAAA

Alignment

ORF - retro_ggor_1346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.98 %
• Parental protein coverage: 77.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LARPCIARKQVEIAQREGAKYVSHGATGKGNDQVRFELSCYSLAPHIKVIAPWRMPEFYNRFKGRNDLME
          LARPCIA.KQ.EI.Q..GAKY.SH.ATG.GN.QVRFEL.CYSLAP.IKVIAPWRMP.FYN..KGRNDLME
Retrocopy LARPCIACKQMEITQWKGAKYMSHSATGNGNNQVRFELICYSLAPQIKVIAPWRMPKFYNQLKGRNDLME

Parental  YAKQHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGLYTKT-QDPAKAPNTPDILEIEFKKGV
          YAKQH.IPIPVTPKN.WS.DENLMHISYEAGI.ENPKNQAPPGLYTKT.QDPAKAPNTPDIL.IEFKKGV
Retrocopy YAKQHRIPIPVTPKNSWSRDENLMHISYEAGIPENPKNQAPPGLYTKT<QDPAKAPNTPDILKIEFKKGV

Parental  PVKVTNVKDGTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRGIYETPAGTILYHAHLDIEAFT
          PVKVTNVKDGTTHQTSLELFMYLNEV.GK.GVG.IDI.ENRFIGMKSRGIY..PA.TILY.AHLD..AFT
Retrocopy PVKVTNVKDGTTHQTSLELFMYLNEVVGKQGVGCIDIMENRFIGMKSRGIYQAPASTILYLAHLDTKAFT

Parental  MDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEGKVQVSVLKGQVYILGRESPLSLYN
          MD.EV.KIKQGLGLKF.ELV.T.FW.SPECEFV.HCIAKSQE.VEGKVQVSVL.GQVYILG.ESPLSLY.
Retrocopy MDQEVHKIKQGLGLKFVELVDTSFWYSPECEFVCHCIAKSQEQVEGKVQVSVLEGQVYILGQESPLSLYK

Parental  EELVSMNVQGDYEPTDATGFININSLRLKEYHRLQSKVTAK
          EE.VSMNVQGDY.P.DATGFINI.SLRLKEYHRLQSKVTAK
Retrocopy EEPVSMNVQGDYQPIDATGFINISSLRLKEYHRLQSKVTAK

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	0.05 RPM	50.35 RPM
SRP007412_cerebellum	0.00 RPM	33.84 RPM
SRP007412_heart	0.00 RPM	20.98 RPM
SRP007412_kidney	0.00 RPM	925.89 RPM
SRP007412_liver	0.05 RPM	400.50 RPM
SRP007412_testis	0.00 RPM	108.68 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_1346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1346 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3175
Pan troglodytes	retro_ptro_2268
Pongo abelii	retro_pabe_2637

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020554	3 retrocopies	retro_cjac_1219, retro_cjac_4038, retro_cjac_4209,
Homo sapiens	ENSG00000130707	14 retrocopies	retro_hsap_2247, retro_hsap_2885, retro_hsap_3109, retro_hsap_3175, retro_hsap_3252, retro_hsap_3564, retro_hsap_3824, retro_hsap_4149, retro_hsap_4182, retro_hsap_4648, retro_hsap_4743, retro_hsap_4934, retro_hsap_820, retro_hsap_985,
Gorilla gorilla	ENSGGOG00000010228	8 retrocopies	retro_ggor_1346 , retro_ggor_1675, retro_ggor_2134, retro_ggor_2403, retro_ggor_2574, retro_ggor_2787, retro_ggor_671, retro_ggor_787,
Myotis lucifugus	ENSMLUG00000006066	2 retrocopies	retro_mluc_1058, retro_mluc_1304,
Mus musculus	ENSMUSG00000076441	1 retrocopy	retro_mmus_135,
Nomascus leucogenys	ENSNLEG00000012500	13 retrocopies	retro_nleu_1088, retro_nleu_1245, retro_nleu_1317, retro_nleu_1381, retro_nleu_1390, retro_nleu_1424, retro_nleu_1701, retro_nleu_1792, retro_nleu_220, retro_nleu_253, retro_nleu_2680, retro_nleu_2764, retro_nleu_625,
Pongo abelii	ENSPPYG00000019692	13 retrocopies	retro_pabe_1963, retro_pabe_2390, retro_pabe_2637, retro_pabe_2696, retro_pabe_2937, retro_pabe_3069, retro_pabe_3197, retro_pabe_3422, retro_pabe_3460, retro_pabe_3521, retro_pabe_3522, retro_pabe_731, retro_pabe_834,
Pan troglodytes	ENSPTRG00000021473	14 retrocopies	retro_ptro_1590, retro_ptro_1951, retro_ptro_2101, retro_ptro_2199, retro_ptro_2268, retro_ptro_2421, retro_ptro_2602, retro_ptro_2821, retro_ptro_2836, retro_ptro_3064, retro_ptro_3158, retro_ptro_3298, retro_ptro_571, retro_ptro_762,