RetrogeneDB ID: retro_ptro_1720

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:182478869..182480413(-)
• Located in intron of: ENSPTRG00000012684

Retrocopy information

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

Parental gene information

• Parental gene symbol: API5
• Ensembl ID: ENSPTRG00000003516
• Aliases: None
• Description: None

Sequence

>retro_ptro_1720
ATGCCGATGGTAGAGGAGCTTTACGGCAACTATGGCATCATGGCCGATACCACGGAGCGAGTGGGCCAGCATAAAGATGC
CTATCAAGTGATACTGGATGGTGTGAAAGGTGGTACTAAGGAAAAACGATTAGCAGCTCAATTTATTCTGAAATTCTTTA
AGCATTTTACAGAATTGGCTGATTCTGCTATCAATGCACAGTTAGACCTCTGTGAAGATGAAGATGTATCTATTTGACGT
CAAGCAATTAAAGAACTGCCTCAATTTACCACTGGAGAAAATCTTCCTCGAGTGGCAGATATACTAATGCAACTTTTGGA
GACAGATGGCTCTGCAGAATTTAACCTAGTGAACAATGCCCTGTTGAGTATATTTAACATGGATGGAAAAGGGACTTTAG
GTTCATTGTTCAGCCAAATACTTCAAGGAGAGGACATTGTTAGAGAACGAGCAATTAAATTCGTTTCTACAAAACTTAAG
ACTTTACCAGATGAAGTATTAACAAAGGAAGTGGAAGAGCTTATACTAACTGAATCCGAACACGTCCTAGAAGATGTGAC
TCATGAAGAATTTGTTCTATTCATGAATTACTGTCTGGGTTAAAAAGCTTACAGACAGTAAGTGGAAGACAGCAACTTGT
AAAGTTGGTGGCTGAACAGGCCGACCTAGAACAACAGACCTTCAATCCCTCAGATCCTGAGTGTGTGGGCAGGCTCTTAC
AGTGCACTCAGCAGGCAGTACCCTTCTTCTCTAAAACTGTCCATTCCACAAGGTCTGTGACATATTTCTGTGAGCAGGTT
CTCCCTAACCTTGGTATCTTGACTACCGCAGTGGAAGGTCTTGACATACAGTTGGAGGTATTGAAATTGTTGGTGGAGAT
GAGTTCATTTTGTGGTGACGTGGAAAAACTAGAAACAAATTTAGGGAAACTATTTGATAAGTTATTGGAATACATGCCCC
TCCCTCCAGAAGAAGCAGAAAATGGAGGGAATGCTGGTGATGAAGAACCCAAACTACAGTTCAGTTATGTGGAATGTTTG
TTGTACAGTTTTCACCAGTTGCGCCAAAAACTTCCAGATTTCTTAATAGCCAAACTGAATGCAGAAAAACTCAAAGATTT
CAAAATCAGGCTGCAATACTTTGCACGAGGCCTGCAAGTTTATATCAGACAACTTCACTTAGCTCTCCAGGGTGAAACAG
GTGAGAACAGAAGAGAACAGAAAACAGAAGAGAACAAAATTAAAGTTGTTGCATTGAAAGCAACAAACAATATCAATGTT
TTAATCAAGGATCTCTTCCACATTCCTCCTTCTTGTAAGAGCACAGTAACACTATCCTGGAAACCTGTACAAAAGGTTGA
GATTGGGCAAAAGAGAGCCAGTGAATATACAACTTCAGGTTCACCACCCCAGAAATCTTCAGCAGGACAAAAAAGAGATG
CCAGGCAGATTTATAATCCTCCCAGTGAGAAATATAGCAGCAATTTGGGCAACTTTAATTATGAGAGGAGCCTTCAGGGA
AAGTAGAGGGGGCCGAGGTTGGGG

Alignment

ORF - retro_ptro_1720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.18 %
• Parental protein coverage: 97.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPTVEELYRNYGILADATEQVGQHKDAYQVILDGVKGGTKEKRLAAQFIPKFFKHFPELADSAINAQLDL
          MP.VEELY.NYGI.AD.TE.VGQHKDAYQVILDGVKGGTKEKRLAAQFI.KFFKHF.ELADSAINAQLDL
Retrocopy MPMVEELYGNYGIMADTTERVGQHKDAYQVILDGVKGGTKEKRLAAQFILKFFKHFTELADSAINAQLDL

Parental  CEDEDVSIRRQAIKELPQFATGENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQI
          CEDEDVSI.RQAIKELPQF.TGENLPRVADIL.QLL.TD.SAEFNLVNNALLSIF.MD.KGTLG.LFSQI
Retrocopy CEDEDVSI*RQAIKELPQFTTGENLPRVADILMQLLETDGSAEFNLVNNALLSIFNMDGKGTLGSLFSQI

Parental  LQGEDIVRERAIKFLSTKLKTLPDEVLTKEVEELILTESKKVLEDVTGEEFVLFM-KILSGLKSLQTVSG
          LQGEDIVRERAIKF.STKLKTLPDEVLTKEVEELILTES..VLEDVT.EEFVLFM...LSGLKSLQTVSG
Retrocopy LQGEDIVRERAIKFVSTKLKTLPDEVLTKEVEELILTESEHVLEDVTHEEFVLFM<ELLSGLKSLQTVSG

Parental  RQQLVELVAEQADLE-QTFNPSDPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNLGTLTTPVE
          RQQLV.LVAEQADLE.QTFNPSDP.CV.RLLQCT.QAVP.FSK.VHSTR.VTYFCEQVLPNLG.LTT.VE
Retrocopy RQQLVKLVAEQADLEQQTFNPSDPECVGRLLQCTQQAVPFFSKTVHSTRSVTYFCEQVLPNLGILTTAVE

Parental  GLDIQLEVLKLLAEMSSFCGDMEKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVECLLY
          GLDIQLEVLKLL.EMSSFCGD.EKLETNL.KLFDKLLEYMPLPPEEAENG.NAG.EEPKLQFSYVECLLY
Retrocopy GLDIQLEVLKLLVEMSSFCGDVEKLETNLGKLFDKLLEYMPLPPEEAENGGNAGDEEPKLQFSYVECLLY

Parental  SFHQLGRKLPDFLTAKLNAEKLKDFKIRLQYFARGLQVYIRQLRLALQGKTGE---ALKTEENKIKVVAL
          SFHQL..KLPDFL.AKLNAEKLKDFKIRLQYFARGLQVYIRQL.LALQG.TGE.....KTEENKIKVVAL
Retrocopy SFHQLRQKLPDFLIAKLNAEKLKDFKIRLQYFARGLQVYIRQLHLALQGETGENRREQKTEENKIKVVAL

Parental  KITNNINVLIKDLFHIPPSYKSTVTLSWKPVQKVEIGQKRASEDTTSGSPPKKSSAGPKRDARQIYNPPS
          K.TNNINVLIKDLFHIPPS.KSTVTLSWKPVQKVEIGQKRASE.TTSGSPP.KSSAG.KRDARQIYNPPS
Retrocopy KATNNINVLIKDLFHIPPSCKSTVTLSWKPVQKVEIGQKRASEYTTSGSPPQKSSAGQKRDARQIYNPPS

Parental  GKYSSNLGNFNYEQ--RGAFRGSRGG
          .KYSSNLGNFNYE....G..RG.R.G
Retrocopy EKYSSNLGNFNYERSLQGK*RGPRLG

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	22.09 RPM
SRP007412_cerebellum	0.04 RPM	44.45 RPM
SRP007412_heart	0.00 RPM	18.33 RPM
SRP007412_kidney	0.00 RPM	26.94 RPM
SRP007412_liver	0.13 RPM	19.31 RPM
SRP007412_testis	0.21 RPM	29.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1720 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1720 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2350
Gorilla gorilla	retro_ggor_1784
Macaca mulatta	retro_mmul_947

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166181	2 retrocopies	retro_hsap_2350, retro_hsap_4893,
Gorilla gorilla	ENSGGOG00000002358	2 retrocopies	retro_ggor_1784, retro_ggor_3055,
Myotis lucifugus	ENSMLUG00000013546	1 retrocopy	retro_mluc_245,
Nomascus leucogenys	ENSNLEG00000017956	1 retrocopy	retro_nleu_352,
Pan troglodytes	ENSPTRG00000003516	2 retrocopies	retro_ptro_1720 , retro_ptro_3261,