RetrogeneDB ID: retro_ptro_3129

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:73878730..73879524(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTGES3L-AARSD1
• Ensembl ID: ENSPTRG00000009230
• Aliases: None
• Description: PTGES3L-AARSD1 readthrough [Source:UniProtKB/TrEMBL;Acc:K7CD23]

Sequence

>retro_ptro_3129
ACCACCACCATAATCTCCTGTGATCCCACGGAGCTGCAGTCAGAAGGGAGCAATGACAAGAAATAAGTGCTGAGCAGTTG
TCATATGGTGCTGGAAGACATGCTACTTTTCCCTGAGGGTGGAAGACAGCCTGATGACGGTGGTACAATCAATGACATCT
CTGTACTGGGAGTGACCCACTCAGGGGCCCAGGCTGATCATTTCACACAGACACCCCTGGATCCTGGAAGCCAAGTCCTG
GTCTGGGTAGACTGGGAGTGGAGGTTTGACCACATGCAGCAGCATTAAAGGCAGCATCTCATCACAGCAGTTGCTGATTA
TCTGTTTGAGTTAAAGACAACATCATGGGAGTTAGGGAAATTTCGGAGTGTGATGCTGGAAAGCCCCTCTGTGAATGCAG
AGAAAATAACCGCCACTGAAAAGAGTGTCAATAAAAATATCAGAGATCAGCTGCTCAACAAAGTATGAGAACTGAGCCTG
AATGATCCTGAGGCGGAGCAGGTGAGAGGCTGGGGCCTGCCAGATGATCATGCTGGGCCCATTGGAATTGTTACCATCAA
GGGTGTTGATTCCAACATGTGCTGTGGGATCCCCATGAGCAATCTCCGTGACTTTCCAGTCATTAAGATTAGGCACCGAG
AAGAGGAAAAGGAATAAAATCAAACTGATATTTCTGGCTGGGAACCAGATGCTGAAATGGATGAAGAGAAGTCATGAAAC
TGAAAGAGCACTGAATCACTCTGCTTAAGTGTGGAGCAGAGGATCACATGGAAGCAGTGAAAAAGCTCCAGAAC

Alignment

ORF - retro_ptro_3129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.0 %
• Parental protein coverage: 57.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TTTVVSCCPAELQTEGSNGKKEVLSGFQVVLEDTVLFPEGGGQPDDRGTINDISVLRVTRRGEQADHFTQ
          TTT..SC.P.ELQ.EGSN.KK.VLS....VLED..LFPEGG.QPDD.GTINDISVL.VT..G.QADHFTQ
Retrocopy TTTIISCDPTELQSEGSNDKK*VLSSCHMVLEDMLLFPEGGRQPDDGGTINDISVLGVTHSGAQADHFTQ

Parental  TPLDPGSQVLVRVDWERRFDHMQQHSGQHLITAVADHLFKLKTTSWELGRFRSAIELDTPSMTAEQVAAI
          TPLDPGSQVLV.VDWE.RFDHMQQH..QHLITAVAD.LF.LKTTSWELG.FRS...L..PS..AE...A.
Retrocopy TPLDPGSQVLVWVDWEWRFDHMQQH*RQHLITAVADYLFELKTTSWELGKFRS-VMLESPSVNAEKITAT

Parental  EQSVNEKIRDRLPVNVRELSLDDPEVEQVSGRGLPDDHAGPIRVVSIEGVDSNMCCGTHVSNLSDLQVIK
          E.SVN..IRD.L...V.ELSL.DPE.EQV.G.GLPDDHAGPI..V.I.GVDSNMCCG...SNL.D..VIK
Retrocopy EKSVNKNIRDQLLNKV*ELSLNDPEAEQVRGWGLPDDHAGPIGIVTIKGVDSNMCCGIPMSNLRDFPVIK

Parental  ILGTE-KGK-KNRTNLIFLAGNRVLKWMERSHGTEKALT-ALLKCGAEDHVEAVKKLQN
          I...E..GK..N...LIFLAGN..LKWM.RSH.TE.AL...LLKCGAEDH.EAVKKLQN
Retrocopy IRHRE<RGK<RNKIKLIFLAGNQMLKWMKRSHETERALN>TLLKCGAEDHMEAVKKLQN

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	1.09 RPM	17.18 RPM
SRP007412_cerebellum	1.04 RPM	29.86 RPM
SRP007412_heart	0.12 RPM	23.93 RPM
SRP007412_kidney	0.60 RPM	15.35 RPM
SRP007412_liver	0.00 RPM	17.38 RPM
SRP007412_testis	0.00 RPM	42.57 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3129 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3129 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3129 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4707

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000266967	1 retrocopy	retro_hsap_4707,
Pan troglodytes	ENSPTRG00000005108	8 retrocopies	retro_ptro_1533, retro_ptro_1945, retro_ptro_2111, retro_ptro_2926, retro_ptro_319, retro_ptro_452, retro_ptro_454, retro_ptro_609,
Pan troglodytes	ENSPTRG00000009230	1 retrocopy	retro_ptro_3129 ,