RetrogeneDB ID: retro_pabe_2384

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:174524207..174525014(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF7
• Ensembl ID: ENSPPYG00000013114
• Aliases: None
• Description: Kruppel-like factor 7 (ubiquitous) [Source:HGNC Symbol;Acc:6350]

Sequence

>retro_pabe_2384
GAGGAGACATGCCTTGAATTGGAATGCTACCTACAGACGGAGCCCAGGAGGATCTCGGAGACCTTTGTTGAGGACTTGGC
CTGTTTGCTCCACGTTTCTCCTCCCCGGTGCATTGAGGAAAGCTTCCGTCGCTTAGACCTCCTGCTGCTCCCCGTGGAAG
TGGCCATCTGTGAGAAGAGCTCAGCAGTAGACATCTTGCTCTCTTGGGGCAAGTTGCTATCTGAGACCTGCCTCAGCCTC
CAGCCGCCAACTCTTCTCTAGACAGCTACACAGCTGTCAACCAGGTCCAGCTCAACACAATGACCTCATTAATGCCCCCA
TTGTCCCCTGAGCTCAGCCGCCATCTGGTCAAAACCTCACAAACTCTCTCTGCCGTGGATGGCACAGTGACGTCGAAACT
AGTGGCCAAGAAGGCTGCTCTCATCTCCATAAAGGGGAAGGGGTCACAACAGCTTCAGCAGCCGTGATGGTGCCAGGGCC
GTTAAGAGTGGACAGAGTGACAGTGACCAAGGAGGGCTAGGGGCTGAAGCATGTCCTGAAAACAAGAAGAGGGTTCACTG
CTGTCAGTTTAACGGGTGCCAGGAAGTTTATACAAAAAGCTCCCACGTAAAGGCCCATCAGAGGACTCACACAGGTGAGA
AGCCTTACAGGTACTCATGGGAGGGATGCTAGTGGCGTTTTGCATGAAGCGATGAGATCACGAGGCACTACGGGAAACAC
ACAGGTGCAAACCTCTTCAAATGCAACCACTGCGACAGGTGTTTTTCCAGGTCTGACCATCTTGCCCTCCCTATGAAGAG
ACATATC

Alignment

ORF - retro_pabe_2384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.88 %
• Parental protein coverage: 89.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QQTCLELERYLQTEPRRISETFGEDLDCFLHASPPPCIEESFRRLDPLLLPVEAAICEKSSAVDILLSRD
          ..TCLELE.YLQTEPRRISETF.EDL.C.LH.SPP.CIEESFRRLD.LLLPVE.AICEKSSAVDILLS..
Retrocopy EETCLELECYLQTEPRRISETFVEDLACLLHVSPPRCIEESFRRLDLLLLPVEVAICEKSSAVDILLSWG

Parental  KLLSETCLSLQP-ASSSLDSYTAVNQAQLNAVTSLTPPSSPELSRHLVKTSQTLSAVDGTVTLKLVAKKA
          KLLSETCLSLQP.A.SSLDSYTAVNQ.QLN..TSL.PP.SPELSRHLVKTSQTLSAVDGTVT.KLVAKKA
Retrocopy KLLSETCLSLQP<ANSSLDSYTAVNQVQLNTMTSLMPPLSPELSRHLVKTSQTLSAVDGTVTSKLVAKKA

Parental  ALSSVKVGG-VATAAAAVTAAG-AVKSGQSDSDQGGLGAEACPENKKRVHRCQFNGCRKVYTKSSHLKAH
          AL.S.K..G.V.TA.AAV...G.AVKSGQSDSDQGGLGAEACPENKKRVH.CQFNGC..VYTKSSH.KAH
Retrocopy ALISIKGKG<VTTASAAVMVPG<AVKSGQSDSDQGGLGAEACPENKKRVHCCQFNGCQEVYTKSSHVKAH

Parental  QRTHTGEKPYKCSWEGCEWRFARSDELTRHYRKHTGAKPFKCNHCDRCFSRSDHLALHMKRHI
          QRTHTGEKPY..SWEGC.WRFA.SDE.TRHY.KHTGA..FKCNHCDRCFSRSDHLAL.MKRHI
Retrocopy QRTHTGEKPYRYSWEGC*WRFA*SDEITRHYGKHTGANLFKCNHCDRCFSRSDHLALPMKRHI

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	4.20 RPM
SRP007412_cerebellum	0.00 RPM	6.44 RPM
SRP007412_heart	0.00 RPM	3.52 RPM
SRP007412_kidney	0.00 RPM	3.15 RPM
SRP007412_liver	0.00 RPM	3.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2384 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2384 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2880
Pan troglodytes	retro_ptro_1948
Gorilla gorilla	retro_ggor_1996

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 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 ,
Pongo abelii	ENSPPYG00000019478	7 retrocopies	retro_pabe_1836, retro_pabe_2020, retro_pabe_2022, retro_pabe_2024, retro_pabe_2027, retro_pabe_2037, retro_pabe_3579,
Pan troglodytes	ENSPTRG00000012850	1 retrocopy	retro_ptro_1948,