RetrogeneDB ID: retro_ptro_1708

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:162199137..162200367(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTA3
• Ensembl ID: ENSPTRG00000011867
• Aliases: None
• Description: None

Sequence

>retro_ptro_1708
ATGGCGGCCAACATGTACCAGGTAGGAGATTTTGTCTACTTTGAGAATTCCTCCAGCAATCCATAAATAATCAGGATAGA
AAATCTCGACAAGACTGCAAGTGGCAACATGGAAGCAAAAGTAGTATGCTTTTACAGATTACGTGATATTTCGAACACAC
TGATAATGCTTATGGAGAAGCATGCTAAAGAAATTGAGGAAGAATCTGAAACAATAGTTGACCTTTACTTGACCAATACT
CAGAAACATCAATCAAAACATAAGTTACTTTCTTTGTCACCCCAATATGAATCTTTGCCTTCAACACATATTAGGGGAAA
ATGCAGTGTTGGCTTATGAATGAGACAGAATCAGTATTGTCATATCTTCATAAAAAGGATACTTTCTTCTACTTATTGAT
CATGACCCCTCATCGAAAATGCTATTAGCTGATGAAGGTGAATTCAGAATGGGACCTAGATATCAAGTAGATGTCCCAGA
AATGCTCATAGAAGGAGAATCAGATGAGAGGGAACAGTGAAAATGGAAAGTTAAAGTTTGGGGATCCAAATAGCCCACTT
AAAGATTGATCAATTAACCAGTTTTTAATTGTAGCAAGTACTATTGGGACACTCCCTAGACCTCTCGATTGCAGCAGTTC
TTTGAGGCAGCCTAGTTTGCATATGAGTACTGCTGCAGCTTCCCAAGACATCACCTTCTTTCATGCTATCAATACATTGT
GTAGACATAGCTATGATTTGAGCAGTGCAATTAGTGTCTCAGTACCACTTGAAGAAGCTGTTTTATGCAGAGATAAATTG
GAAGAATGGTCAGCCTCTTAAGCTAGCTTATTCGAAGAGGTACTGGAAAAAATATGGCAAAGACTTCAACGACATATGCC
AAAAATTTTTCCCTTGGAAATCATTGACTAGCATCACTGAGTGTTATTTCTTGTGGAGAACTACTGACAGATATGTGCAA
CAGAAATGGTTAAAAGCAGCAGAAACTGAGAGTAAGCTGAAACAAGTATATATCCCAATTTACAGGAAACCAAATCCCAA
CCAAATATCTACCAGCAATGGCAAGCCTGGTGCTATGAGTGAAACCATGAGGTTGACATTCCTGCCTCAGAATCCCCTTG
TAGTGCAAGCCTGGGAGGGCTGCTGTGCTACACAGTCTAACCAGTAGTATTCTTGGGGCCCACCTAATATGCAGTGCAAT
TTGTTGGCTTTATTGAGAAAAATATGGAGA

Alignment

ORF - retro_ptro_1708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.22 %
• Parental protein coverage: 79.81 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAANMYRVGDYVYFENSSSNPYLIRRIEELNKTASGNVEAKVVCFYRRRDISNTLIMLADKHAKEIEEES
          MAANMY.VGD.VYFENSSSNP..IR.IE.L.KTASGN.EAKVVCFYR.RDISNTLIML..KHAKEIEEES
Retrocopy MAANMYQVGDFVYFENSSSNP*IIR-IENLDKTASGNMEAKVVCFYRLRDISNTLIMLMEKHAKEIEEES

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

Parental  SLKTLLADKGEIRVGPRYQADIPEMLLEGESDEREQSKLEVKVW-DPNSPLTDRQIDQFLVVARAVGTFA
          S.K.LLAD.GE.R.GPRYQ.D.PEML.EGESDEREQ.K..VKVW.DPNSPL.D..I.QFL.VA...GT..
Retrocopy SSKMLLADEGEFRMGPRYQVDVPEMLIEGESDEREQ*KWKVKVW>DPNSPLKD*SINQFLIVASTIGTLP

Parental  RALDCSSSVRQPSLHMSAAAASRDITLFHAMDTLYRHSYDLSSAISVLVPLGGPVLCRDEMEEWSASEAS
          R.LDCSSS.RQPSLHMS.AAAS.DIT.FHA..TL.RHSYDLSSAISV.VPL...VLCRD..EEWSAS.AS
Retrocopy RPLDCSSSLRQPSLHMSTAAASQDITFFHAINTLCRHSYDLSSAISVSVPLEEAVLCRDKLEEWSAS*AS

Parental  LFEEALEK-YGKDFNDIRQDFLPWKSLTSIIEYYYMWKTTDRYVQQKRLKAAEAESKLKQVYIPTYSKPN
          LFEE.LEK.YGKDFNDI.Q.F.PWKSLTSI.E.Y..W.TTDRYVQQK.LKAAE.ESKLKQVYIP.Y.KPN
Retrocopy LFEEVLEK>YGKDFNDICQKFFPWKSLTSITECYFLWRTTDRYVQQKWLKAAETESKLKQVYIPIYRKPN

Parental  PNQISTSNGKPGAVNGAVGTTFQPQNPLLGRACESCYATQSHQWYSWGPPNMQCRLCAICWLYWK
          PNQISTSNGKPGA.......TF.PQNPL...A.E.C.ATQS.Q.YSWGPPNMQC.L.A.....W.
Retrocopy PNQISTSNGKPGAMSETMRLTFLPQNPLVVQAWEGCCATQSNQ*YSWGPPNMQCNLLALLRKIWR

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	11.24 RPM
SRP007412_cerebellum	0.00 RPM	12.37 RPM
SRP007412_heart	0.00 RPM	9.44 RPM
SRP007412_kidney	0.05 RPM	15.59 RPM
SRP007412_liver	0.03 RPM	5.56 RPM
SRP007412_testis	0.00 RPM	52.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1708 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1708 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1708 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2337
Gorilla gorilla	retro_ggor_1773
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 ,