RetrogeneDB ID: retro_ggor_1773

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:45499180..45500359(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTA3
• Ensembl ID: ENSGGOG00000006895
• Aliases: None
• Description: None

Sequence

>retro_ggor_1773
ATGGCGGCCAACATGTACCAGGTAGGAGATTTTGTCTACTTTGAGAATTCCTCCAGCAATCCATAAATAATCAGGATAGA
AAATCTCGACAAGACTGCAAGTGGCAACATGGAAGCAAAAGTAGTATGCTTTTACAGATTACGTGATATTTCCAACACAC
TGATAATGCTTGTGGAGAAGCATGCTAAAGAAATTGAGGAATAATCTGAAACAATAGTTGACCCTTACTTGACCAATACT
CAGAAACATCAATCAAAACATAAGTTACTTTCTTTGTCACCCCAATATGAATCTTTGCCTTCAACACATATTAGGGGAAA
ATGCAGTGTTGGCTTATGAATGAGACAGAATCAGTATTGTCATATCTTCATAAAAAGGATACTTTCTTCTACTTATTGAT
CATGATCCCTCATCGAAAACACTATTAGCTGATGAAGATGAATTCAGAATGGGACCTAGATATCAAGTAGATGTCCCAGA
AATGCTCATAGAAGGAGAATCAGATGAGAGGGAACAGTGAAAATGGAAAGTTAAAGTTTGGGGATCCAAATAGCCCACTT
AAAGATTGATCAATTAACTAGTTTTTAATTGTAGCAAGTACTATTGGGACACTCCCTAGACCTCTCGATTGCAGCAGTTC
TTTGAGGCAGCCTAGTTTGCATATGAGTGCTGCTGCAGCTTCCCAAGACATCACCCTCTTTCATGCTATCGATGCATTGT
GTAGACATAGCTATGATTTGAGCAGTGCAATTAGTGTCTCAGTACCACTTGAAGAAGCTGTTTTATGCAGAGATAAATTG
GAAGAATGGTCAGCCTCTTAAGCTAGCTTATTCGAAGAGGTACTGGAAAAAATATGGCAAAGACTTCAACGACATATGCC
AAAACTTTTTCCCTTGGAAATCATTGACTAGCATCACTGAATGTTATTTCTTGTGGAGAACTACTGACAGATATGTGCAA
CAGAAATGGTTAAAAGCAGCAGAAACTGAGAGTAAGCTGAAACAAGTATATATCCCAGTTTACAGCAAACCAAATCCCAA
CCAAATATCTACCAGCAATGGCAAGCCTGGTGTTATGAGTGAAACCATGAGGTTGACATTCCTGCCTCAGAATCCGCTTG
TAGTGCAAGCCTGGGAGGGCTGCTGTGCTACACAGTCTAACCAGTAGTATTCTTGGGGC

Alignment

ORF - retro_ggor_1773 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.5 %
• Parental protein coverage: 65.61 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAANMYRVGDYVYFENSSSNPYLIRRIEELNKTASGNVEAKVVCFYRRRDISNTLIMLADKHAKEIEEES
          MAANMY.VGD.VYFENSSSNP..IR.IE.L.KTASGN.EAKVVCFYR.RDISNTLIML..KHAKEIEE.S
Retrocopy MAANMYQVGDFVYFENSSSNP*IIR-IENLDKTASGNMEAKVVCFYRLRDISNTLIMLVEKHAKEIEE*S

Parental  ETTVEADLTDKQKHQLKHRELFLSRQYESLPATHIRGKCSVAL-LNETESVLSYLDKEDTFFYSLV-YDP
          ET.V...LT..QKHQ.KH..L.LS.QYESLP.THIRGKCSV.L..NETESVLSYL.K.DTFFY.L...DP
Retrocopy ETIVDPYLTNTQKHQSKHKLLSLSPQYESLPSTHIRGKCSVGL<MNETESVLSYLHKKDTFFYLLI<HDP

Parental  SLKTLLADKGEIRVGPRYQADIPEMLLEGESDEREQSKLEVKVW-DPNSPLTDRQIDQFLVVARAVGTFA
          S.KTLLAD..E.R.GPRYQ.D.PEML.EGESDEREQ.K..VKVW.DPNSPL.D..I..FL.VA...GT..
Retrocopy SSKTLLADEDEFRMGPRYQVDVPEMLIEGESDEREQ*KWKVKVW>DPNSPLKD*SIN*FLIVASTIGTLP

Parental  RALDCSSSVRQPSLHMSAAAASRDITLFHAMDTLYRHSYDLSSAISVLVPLGGPVLCRDEMEEWSASEAS
          R.LDCSSS.RQPSLHMSAAAAS.DITLFHA.D.L.RHSYDLSSAISV.VPL...VLCRD..EEWSAS.AS
Retrocopy RPLDCSSSLRQPSLHMSAAAASQDITLFHAIDALCRHSYDLSSAISVSVPLEEAVLCRDKLEEWSAS*AS

Parental  LFEEALE-KYGKDFNDIRQDFLPWKSLTSIIEYYYMWKTTDRYVQQKRLKAAEAESKLKQVYIPTY-KPN
          LFEE.LE.KYGKDFNDI.Q.F.PWKSLTSI.E.Y..W.TTDRYVQQK.LKAAE.ESKLKQVYIP.Y.KPN
Retrocopy LFEEVLE>KYGKDFNDICQNFFPWKSLTSITECYFLWRTTDRYVQQKWLKAAETESKLKQVYIPVYSKPN

Parental  PNQISTSNGKPGAVNGAVGTTFQPQNPLLGRACESCYGQLSIGNCSGSWG
          PNQISTSNGKPG........TF.PQNPL...A.E.C....S..N...SWG
Retrocopy PNQISTSNGKPGVMSETMRLTFLPQNPLVVQAWEGCCATQS--NQ*YSWG

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	17.02 RPM
SRP007412_cerebellum	0.04 RPM	7.25 RPM
SRP007412_heart	0.00 RPM	1.88 RPM
SRP007412_kidney	0.04 RPM	7.93 RPM
SRP007412_liver	0.08 RPM	4.59 RPM
SRP007412_testis	0.31 RPM	46.93 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_1773 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1773 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2337
Pan troglodytes	retro_ptro_1708
Pongo abelii	retro_pabe_2115

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014614	1 retrocopy	retro_cjac_1177,
Homo sapiens	ENSG00000057935	1 retrocopy	retro_hsap_2337,
Gorilla gorilla	ENSGGOG00000006895	1 retrocopy	retro_ggor_1773 ,
Nomascus leucogenys	ENSNLEG00000016680	1 retrocopy	retro_nleu_1688,
Pan troglodytes	ENSPTRG00000011867	1 retrocopy	retro_ptro_1708,