RetrogeneDB ID: retro_ggor_1947

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:74623913..74625280(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD12
• Ensembl ID: ENSGGOG00000014761
• Aliases: None
• Description: None

Sequence

>retro_ggor_1947
ATGGCAGACGGCCACTTGGAGTGGGCTGACAGGCGCATCTTCAAAATGGAAGTGGACTACAACGCCACGGTAGATCAGTG
CCTACCCGAGTGTGAGAAGCTGGCCAAGGAAGGAAGACTTCAAGAAGTCATGGAAACCCTTCTCTCTTTGGAAAAACAGA
CTCGTACTGCTTCTGATATGGGGTCAACATCCCAAATCTTAGTTGCAGTAGTGAAGATGTGCTATGAGGCTAAATAATGG
GATTTACTTAATGAAAATATTACACTTTTGTCCAAAAGGCGGAGTCAATTAATACAAGCTGTTGCCAAAATGGTTCAGTA
GTACTGTATTTATGTTGAGGAAATCACAGACCTTCCTATCAAACTTCAATTAACTGATACTCTATGAATGGTTACCGAAG
GCAAGATTTATGTTGAAATTGAGTGTGCTTGACTGACTAAAACATTAGCAACTATAAAAGAACAAAATGGTGATGTGAAA
GAGGCAGCCTCCGTTTATAGGAGCTACAGGTGGAAACCTATGGATCAATGCAAAAGAAAGAGCAAGTGGAATTTATTTTG
GAGCAAATGAGGCTCTGCCTAGCTGTAAAGGATTACATTCGAACATAAATCATCAGTAAGAAAATTAACACCAAGTTTTT
CCAGGAAGAAAATACAGCGAAATTAAAGTTGAAGTACGATAATTTAATGACTCAGCTGGATGAACACGAGGGATCCTATT
TATTTATTTGTAAGCACTACAGAGCAATATATAATACTCCCTGTATACAGGCAGAAAGTGAAAAATGGCAGCAGGCTATG
AAGAGTGTTGTACCCTATGTTACCCTGGCTCCTTTTGACAATGAACAGTCAGATTTGGTTCACCGAATAAGTGGTGACAA
GAAGTCAGAAGAAATTCCCAAATACAAGGATCTTCTAAAACTTTTCACCACAATGGAGTTGATGCGTTGGTCCACACTTG
TGGAGGACTATGAAATGGAATTAAGCAAAGGTTCCGTTGGCAGTCCTGCAACTGATGCTTTTGGTTCTACAGAGGAAGGC
GAAAAAAGGTGGAAAGATTTGAGTAACAGAGTTGTTGAACATAATATTAGAATAATGGCCAAGTATTATACTCGGATGAC
AATGAAAAGGATGGTACAGCTTCTGGATCTATCTGTTGATGAGTCCGAAGCCTTTCTCTCAAATCTAGTAGTTAACAAGA
CCATATTTGCTAAAGTAGACAGATTAGCAGGAATTAACAACGTCCAGAGACCCAAGGATCCAAATAATTTATGAAATGAC
TGGTCTCAGAAACTGAACTCATTAATGTCTCTGGTTAACAAAACTACACATCTCATAGCTAAAGAGGAGATGATACATAA
TCTACAA

Alignment

ORF - retro_ggor_1947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDMVSTSRILVAV
          MADG..E.AD.RI.KMEVDY.ATVDQ.LPEC.KLAKEGRLQEV.ETLLSLEKQTRTASDM.STS.ILVAV
Retrocopy MADGHLEWADRRIFKMEVDYNATVDQCLPECEKLAKEGRLQEVMETLLSLEKQTRTASDMGSTSQILVAV

Parental  VKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTLRMVTEGKIYVEI
          VKMCYEAK.WDLLNENI.LLSKRRSQL.QAVAKMVQ..C.YVEEITDLPIKL.L.DTL.MVTEGKIYVEI
Retrocopy VKMCYEAK*WDLLNENITLLSKRRSQLIQAVAKMVQ*YCIYVEEITDLPIKLQLTDTL*MVTEGKIYVEI

Parental  ERARLTKTLATIKEQNGDVKEAASILQ-ELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKI
          E.A.LTKTLATIKEQNGDVKEAAS....ELQVETYGSM.KKE.VEFILEQMRLCLAVKDYIRT.IISKKI
Retrocopy ECA*LTKTLATIKEQNGDVKEAASVYR<ELQVETYGSMQKKEQVEFILEQMRLCLAVKDYIRT*IISKKI

Parental  NTKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPF
          NTKFFQEENT.KLKLKY.NLM.QLD.HEGSYL.ICKHYRAIY.TPCIQAESEKWQQA.KSVV.YV.LAPF
Retrocopy NTKFFQEENTAKLKLKYDNLMTQLDEHEGSYLFICKHYRAIYNTPCIQAESEKWQQAMKSVVPYVTLAPF

Parental  DNEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEK
          DNEQSDLVHRISGDKK.EEIPKYKDLLKLFTTMELMRWSTLVEDY.MEL.KGS..SPATD.FGSTEEGEK
Retrocopy DNEQSDLVHRISGDKKSEEIPKYKDLLKLFTTMELMRWSTLVEDYEMELSKGSVGSPATDAFGSTEEGEK

Parental  RWKDLKNRVVEHNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPK
          RWKDL.NRVVEHNIRIMAKYYTR.TMKRM.QLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGI.N.QRPK
Retrocopy RWKDLSNRVVEHNIRIMAKYYTRMTMKRMVQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGINNVQRPK

Parental  DPNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ
          DPNNL.NDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ
Retrocopy DPNNL*NDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ

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	0.00 RPM	24.12 RPM
SRP007412_cerebellum	0.00 RPM	13.59 RPM
SRP007412_heart	0.00 RPM	3.56 RPM
SRP007412_kidney	0.00 RPM	15.42 RPM
SRP007412_liver	0.00 RPM	13.11 RPM
SRP007412_testis	0.00 RPM	48.90 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_1947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1947 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2801
Pan troglodytes	retro_ptro_1898
Callithrix jacchus	retro_cjac_1400

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008691	2 retrocopies	retro_cjac_1400, retro_cjac_2793,
Homo sapiens	ENSG00000197170	1 retrocopy	retro_hsap_2801,
Gorilla gorilla	ENSGGOG00000014761	1 retrocopy	retro_ggor_1947 ,
Loxodonta africana	ENSLAFG00000010876	1 retrocopy	retro_lafr_467,
Nomascus leucogenys	ENSNLEG00000001265	1 retrocopy	retro_nleu_1541,
Pongo abelii	ENSPPYG00000008565	1 retrocopy	retro_pabe_2223,
Pan troglodytes	ENSPTRG00000022722	1 retrocopy	retro_ptro_1898,
Tupaia belangeri	ENSTBEG00000014760	1 retrocopy	retro_tbel_443,
Tarsius syrichta	ENSTSYG00000013154	1 retrocopy	retro_tsyr_1670,