RetrogeneDB ID: retro_ptro_1948

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:174770598..174771400(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF7
• Ensembl ID: ENSPTRG00000012850
• Aliases: None
• Description: None

Sequence

>retro_ptro_1948
GAGGAGACATGCCTTGAATTGGAACGCTACCTACAGACGGAGCCCAGAAGGATCTCGGAGACCTTTGGTGAGGACTTGGC
CTGTTTGCTCCACGCTTCTCCTCCCCGGTGCATTGAGGAAAGCTTCTGTCGCTTAGACCTCCTGCTGCTCCCCGTGGAAG
CGGCCATCTGTCAGAAAAGCTCAGCAGTCTTGCTCTCTCGGGGCAAGTTGCTATCTGAGACCTGCCTCAGCCTCCAGCCG
CCAACTCTTCTCTAGACAGCTACGCAGCTGTCAACCAGGTCCAGCTCAACACAATGACCTCATTAATGCCCCCACTGTCC
CCTGAGCTCAGCCACCATCTGGTCAAAACCTCACAAACTCTCTCTGCCGTGGATGGCACGGTGACGTTGAAACTAGTGGC
CAAGAAGGCTGCTCTCATCTCCGTAAAGGTGGGAGGGGTCACAACAGCTTCAGCAGCTGTGATGGTGCCAGGGCCGTTAA
GAGTGGACAGGGCGACAGTGACCAAGGAGGGCTAGGGGCTGAAGCATGTCCTGAAAACAAGAAGAGGGTTCACTGCTGTC
AGTTTAACGGGTGCCAGGAAGTTTATACAAAAAGCTCCCCCTTAAAGGCCCATCAGAAGACTCACACAGGTGAGAAGCCT
TACAGGTACTCATGGGAGGGATGCTAGTGGAGTTTTGCATGAAGCGATGAGCTCACGAGGCACTACGGGAAACACACAGG
TGCAAACTTCTTCAAATGCAACCACTGCAACAGGTGTTTTTCTAGGTCTGACCATCTTGCCCTCCCTATGAAGAAACATA
TC

Alignment

ORF - retro_ptro_1948 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.82 %
• Parental protein coverage: 89.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QQTCLELERYLQTEPRRISETFGEDLDCFLHASPPPCIEESFRRLDPLLLPVEAAICEKSSAVDILLSRD
          ..TCLELERYLQTEPRRISETFGEDL.C.LHASPP.CIEESF.RLD.LLLPVEAAIC.KSSAV..LLSR.
Retrocopy EETCLELERYLQTEPRRISETFGEDLACLLHASPPRCIEESFCRLDLLLLPVEAAICQKSSAV--LLSRG

Parental  KLLSETCLSLQP-ASSSLDSYTAVNQAQLNAVTSLTPPSSPELSRHLVKTSQTLSAVDGTVTLKLVAKKA
          KLLSETCLSLQP.A.SSLDSY.AVNQ.QLN..TSL.PP.SPELS.HLVKTSQTLSAVDGTVTLKLVAKKA
Retrocopy KLLSETCLSLQP<ANSSLDSYAAVNQVQLNTMTSLMPPLSPELSHHLVKTSQTLSAVDGTVTLKLVAKKA

Parental  ALSSVKVGGVATAAAAVTAAG-AVKSGQSDSDQGGLGAEACPENKKRVHRCQFNGCRKVYTKSSHLKAHQ
          AL.SVKVGGV.TA.AAV...G.AVKSGQ.DSDQGGLGAEACPENKKRVH.CQFNGC..VYTKSS.LKAHQ
Retrocopy ALISVKVGGVTTASAAVMVPG<AVKSGQGDSDQGGLGAEACPENKKRVHCCQFNGCQEVYTKSSPLKAHQ

Parental  RTHTGEKPYKCSWEGCEWRFARSDELTRHYRKHTGAKPFKCNHCDRCFSRSDHLALHMKRHI
          .THTGEKPY..SWEGC.W.FA.SDELTRHY.KHTGA..FKCNHC.RCFSRSDHLAL.MK.HI
Retrocopy KTHTGEKPYRYSWEGC*WSFA*SDELTRHYGKHTGANFFKCNHCNRCFSRSDHLALPMKKHI

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	0.05 RPM	12.12 RPM
SRP007412_cerebellum	0.00 RPM	33.66 RPM
SRP007412_heart	0.00 RPM	20.43 RPM
SRP007412_kidney	0.03 RPM	21.65 RPM
SRP007412_liver	0.00 RPM	9.33 RPM
SRP007412_testis	0.00 RPM	12.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1948 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1948 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1948 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2880
Gorilla gorilla	retro_ggor_1996
Pongo abelii	retro_pabe_2384

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000118263	1 retrocopy	retro_hsap_2880,
Gorilla gorilla	ENSGGOG00000009338	1 retrocopy	retro_ggor_1996,
Nomascus leucogenys	ENSNLEG00000007123	1 retrocopy	retro_nleu_620,
Pongo abelii	ENSPPYG00000013114	1 retrocopy	retro_pabe_2384,
Pan troglodytes	ENSPTRG00000012850	1 retrocopy	retro_ptro_1948 ,
Pan troglodytes	ENSPTRG00000021957	1 retrocopy	retro_ptro_1104,
Pan troglodytes	ENSPTRG00000039565	2 retrocopies	retro_ptro_111, retro_ptro_2968,