RetrogeneDB ID: retro_ptro_2753

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:54240660..54241815(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT11
• Ensembl ID: ENSPTRG00000016192
• Aliases: None
• Description: None

Sequence

>retro_ptro_2753
ATATTCTGTGTGGGGGAAACTGGAATTAGAAAATCAACACTGACTGACACATTGTTTAATACTAATTTTGAAGACTATGA
ATCCTCACATTTTTGCCCAAATGTTAAACTTAAAGCTCAGACATATGAACTCCAGGAAAGTAATGTTCGATTGAAATTGA
CCATTGTGAATACAGTGGGATTTGGTGACCAAATAAATAAAGAAGAGAGCTACCAACCGATAGCTGACTACATAGATGCT
CAGTTTGAGGCCTATCTCCAAGAATAACTGAAGATTAAACATTCTCTCTTTACCTACCATGATTCTCGCATCCGTTTGTG
CCTCTACTTCATTTCACCGACAGGCCACTCTCTGAAGACACTTGATCTCTTAACCATGAAGAACCTTGACAGCAAGGTAA
ACATTATACCAGTGATTGCCAAAGCAGATACGGTTTCTAAAACTGAATTACATAAGTTTAAGATCAAGTTCATGAGTGAA
TTGGTCAGCAATGGCGTCCAGATATACCAGTTCCCAACGGATGATGACACTATTGCTAAGGTCAACGCTGCAATGAATGG
ACAGATGCCGTTTGCTGTTGTGGGAAGTATGGATGAGGTAAAAGTCGGAAACAAGATGGTTAAAGCTCGCCAGTACCCTT
GGGGTGTTGTACAAGTGGAAAATGAAAACCACTGTGACTTTGTAAAGCTGCGGGAAATGTTCATTTGTACAAATATGGAG
GACCTGCGATAGCAGACCCATACCAGGCACTATGAGCTTTACAGGCGCTGCAAACTGGAGGAAATGGGCTTTACAGATGT
GGGCCCAGAAAACAAGCCGGTCAGTCTTCAAGAGACCTATGAAGCCAAAAGACATGAGTTCCATGGTGAACGTCAGAGGA
AGGAAGAAGAAATGAAACAGATGTTTGTGCAGCCAGTGAAGGAGAAAGAAGCCATATTGAAAGAAGCTGAGAGAGAGCTA
CAGGCCAAATTTGAGCACCTTAAGAGACTTCACCAAGAAGAGAGAATGAAGCTTGAAGAACAGAGAAGACTTTTGGAAGA
AGAAATAATTGCTTTCTCTAAAAAGAAAGCTACCTCCGAGATATTTCACAGCCAGTCCTTTCTGGCAACAGGCAGCAACC
TGAGTAAGGACAAGGACCGTAAGAACTCCAATTTT

Alignment

ORF - retro_ptro_2753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.13 %
• Parental protein coverage: 89.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILCVGETGIGKSTLMDTLFNTKFESDPATHNEPGVRLKARSYELQESNVRLKLTIVDTVGFGDQINKDDS
          I.CVGETGI.KSTL.DTLFNT.FE.....H..P.V.LKA..YELQESNVRLKLTIV.TVGFGDQINK..S
Retrocopy IFCVGETGIRKSTLTDTLFNTNFEDYESSHFCPNVKLKAQTYELQESNVRLKLTIVNTVGFGDQINKEES

Parental  YKPIVEYIDAQFEAYLQEELKIKRSLFNYHDTRIHACLYFIAPTGHSLKSLDLVTMKKLDSKVNIIPIIA
          Y.PI..YIDAQFEAYLQE.LKIK.SLF.YHD.RI..CLYFI.PTGHSLK.LDL.TMK.LDSKVNIIP.IA
Retrocopy YQPIADYIDAQFEAYLQE*LKIKHSLFTYHDSRIRLCLYFISPTGHSLKTLDLLTMKNLDSKVNIIPVIA

Parental  KADTIAKNELHKFKSKIMSELVSNGVQIYQFPTDEETVAEINATMSVHLPFAVVGSTEEVKIGNKMAKAR
          KADT..K.ELHKFK.K.MSELVSNGVQIYQFPTD..T.A..NA.M....PFAVVGS..EVK.GNKM.KAR
Retrocopy KADTVSKTELHKFKIKFMSELVSNGVQIYQFPTDDDTIAKVNAAMNGQMPFAVVGSMDEVKVGNKMVKAR

Parental  QYPWGVVQVENENHCDFVKLREMLIRVNMEDLREQTHTRHYELYRRCKLEEMGFKDTDPDSKPFSLQETY
          QYPWGVVQVENENHCDFVKLREM.I..NMEDLR.QTHTRHYELYRRCKLEEMGF.D..P..KP.SLQETY
Retrocopy QYPWGVVQVENENHCDFVKLREMFICTNMEDLR*QTHTRHYELYRRCKLEEMGFTDVGPENKPVSLQETY

Parental  EAKRNEFLGELQKKEEEMRQMFVMRVKEKEAELKEAEKELHEKFDLLKRTHQEEKKKVEDKKKELEEEVN
          EAKR.EF.GE.Q.KEEEM.QMFV..VKEKEA.LKEAE.EL..KF..LKR.H...................
Retrocopy EAKRHEFHGERQRKEEEMKQMFVQPVKEKEAILKEAERELQAKFEHLKRLHXXXXXXXXXXXXXXXXXII

Parental  NFQKKKAAAQLLQSQAQQSGAQQTKKDKDKKNASF
          .F.KKKA......SQ..........KDKD.KN..F
Retrocopy AFSKKKATSEIFHSQSFLATGSNLSKDKDRKNSNF

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	0.34 RPM	65.17 RPM
SRP007412_cerebellum	0.18 RPM	61.27 RPM
SRP007412_heart	2.33 RPM	34.22 RPM
SRP007412_kidney	2.35 RPM	78.22 RPM
SRP007412_liver	2.42 RPM	30.77 RPM
SRP007412_testis	29.51 RPM	12.86 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2753 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2753 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2753 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4060
Gorilla gorilla	retro_ggor_2728
Pongo abelii	retro_pabe_3335

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003906	1 retrocopy	retro_chof_1543,
Callithrix jacchus	ENSCJAG00000014744	1 retrocopy	retro_cjac_2336,
Monodelphis domestica	ENSMODG00000011825	1 retrocopy	retro_mdom_224,
Oryctolagus cuniculus	ENSOCUG00000001289	1 retrocopy	retro_ocun_1758,
Otolemur garnettii	ENSOGAG00000005210	1 retrocopy	retro_ogar_2831,
Pan troglodytes	ENSPTRG00000016192	1 retrocopy	retro_ptro_2753 ,
Pan troglodytes	ENSPTRG00000019080	2 retrocopies	retro_ptro_2585, retro_ptro_2853,