RetrogeneDB ID: retro_ptro_1483

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:19083464..19085053(+)
• Located in intron of: ENSPTRG00000014085

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLHL12
• Ensembl ID: ENSPTRG00000001861
• Aliases: None
• Description: None

Sequence

>retro_ptro_1483
GTAGAGCAGAAAGACTTTCCTGCCCATGAGATTGTGCTGGCTGCCTGTAGTGATTACTTCTGTGCCATGTTCACTAGTGA
GCTTTCACAGAAGGGGAAACCCTATGTTGACATCCAAGGTTTGACTGCCTCTACCATGGAAATTTTATTGGACTTTGTGT
ACACGGAAACAGTACATGTGACATGGAGAATGTACAGGAACTGCTTCCTGCAGCCTGTCTGCTTCAGTTGAAAGGTGTGA
AACAAGCCTGCTGTGAGTTCTTAGAAAGTCAGTTGGACCCTTCTAATTGCCTGGGTATTAGGGATTTTGCTGAAACCCAC
AATTGTGTTGACCTGACACAAGCAGCTGAGGTTTTTAGCCAGAAGAATTTTCCTGAAGTGGTACAGCATGAAGAGTTCAT
TCTTCTGAGGCAAGGAGAGGTGGAAAAGCTAATCAAGTGCAATGAAATTCAGGTGGATCCTGAAGAACCAGTCTTTGAGG
CTGTCATCAGTTGGGTGAAGCATGCCAAGAAAGAGCAGAAAGAATCCTTGCCCAACCTGCTACAGTATATGCAGATGCCC
CTGCTAATCCTCAGGTATATCACAGATGTAATAGATGCTGAGGCTTTCATCCGCTGTGGTTTACAATGCAAGGATCTGGT
TGATGAAGCAAAGAAGTTTCATCTGAGGCCTGAACTTCAGAGTCAGATGCAGGGACCCAGGACAAGGGCTCGCCTAGGAG
CCAATGAAGTGCTTTTGGTGGCTGCGGGCTTCGGAAGCCAGCAGTCTCCCATCGATGCAGTAGAGAAATATGACCCCAAG
ACTCAGGAGTGGAGCTTTTTGCCAAGCATCACTTGTAAGAGATGTTATGTGGCCTCAGTGTCCCTACATGACCAGATCTA
CGTCATTGGTGGCTATGATGGTCGTTCCAGCCTTAGTTCAGTGGAATGTCTAGACTACACAGCAGATGAGGAAGGGGTCT
GGTATTCTGTGGCCCCTATGAATGTCTGATGAGGTCTTGCTGGAGCCACCACCCTGGGAGATTTGATCTATGTCTCTGAA
GGCTTTGATGGAAGCAGGCGTCACACCAGTATGGAGCGGTATGATCCAAACATTGACCAGTGGAGCATGCTGGGAGATAT
GCAGACAGCCCGGGAAGGTGCCGGACTCGTAGTGGCCAGTGGAGTGATCCACTGTCTAGGAGGATATGACGGCTTGAATA
TCTTAAATTCAGTTGAGAAATATGACCCTCATACAGGACACTGGACTAATGTTACACCAATGGCCACCAAGCGTTCTGGT
GCAGGAGTAGCCCTGCTGAATGACCGTATTTATGTGGTGGGGAGATTTGATGGTACAGCCCACCTTTCTTCCGTTGAAGC
ATACAACATTCGCACTGATTCCCGGACAACTGCCACCAGTATGACCACTCCACGATGCTATGTAGGGGCCACAGTGCTTC
GGGGGAGACTCTATGCAATTGCAGGATATGAAGGTAAGTCCCTGCTAAGTAGCATTGAATGTTACAACCCTATCATCGAC
AGCTGGGAAGTCGTGACATCCATGGGAACCCAGCGCTGTGATGCTGGTGTGTGTGTTCTCCACAAGAAG

Alignment

ORF - retro_ptro_1483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 93.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VEQKDFPAHRIVLAACSDYFCAMFTSELSEKGKPYVDIQGLTASTMEILLDFVYTETVHVT-VENVQELL
          VEQKDFPAH.IVLAACSDYFCAMFTSELS.KGKPYVDIQGLTASTMEILLDFVYTETVHVT..ENVQELL
Retrocopy VEQKDFPAHEIVLAACSDYFCAMFTSELSQKGKPYVDIQGLTASTMEILLDFVYTETVHVT<MENVQELL

Parental  PAACLLQLKGVKQACCEFLESQLDPSNCLGIRDFAETHNCVDLMQAAEVFSQKHFPEVVQHEEFILLSQG
          PAACLLQLKGVKQACCEFLESQLDPSNCLGIRDFAETHNCVDL.QAAEVFSQK.FPEVVQHEEFILL.QG
Retrocopy PAACLLQLKGVKQACCEFLESQLDPSNCLGIRDFAETHNCVDLTQAAEVFSQKNFPEVVQHEEFILLRQG

Parental  EVEKLIKCDEIQVDSEEPVFEAVINWVKHAKKEREESLPNLLQYVRMPLLTPRYITDVIDAEPFIRCSLQ
          EVEKLIKC.EIQVD.EEPVFEAVI.WVKHAKKE..ESLPNLLQY..MPLL..RYITDVIDAE.FIRC.LQ
Retrocopy EVEKLIKCNEIQVDPEEPVFEAVISWVKHAKKEQKESLPNLLQYMQMPLLILRYITDVIDAEAFIRCGLQ

Parental  CRDLVDEAKKFHLRPELRSQMQGPRTRARLGANEVLLVVGGFGSQQSPIDVVEKYDPKTQEWSFLPSITR
          C.DLVDEAKKFHLRPEL.SQMQGPRTRARLGANEVLLV..GFGSQQSPID.VEKYDPKTQEWSFLPSIT.
Retrocopy CKDLVDEAKKFHLRPELQSQMQGPRTRARLGANEVLLVAAGFGSQQSPIDAVEKYDPKTQEWSFLPSITC

Parental  KRRYVASVSLHDRIYVIGGYDGRSRLSSVECLDYTADEDGVWYSVAPMNVRRGLAGATTLGDMIYVSGGF
          KR.YVASVSLHD.IYVIGGYDGRS.LSSVECLDYTADE.GVWYSVAPMNV..GLAGATTLGD.IYVS.GF
Retrocopy KRCYVASVSLHDQIYVIGGYDGRSSLSSVECLDYTADEEGVWYSVAPMNV**GLAGATTLGDLIYVSEGF

Parental  DGSRRHTSMERYDPNIDQWSMLGDMQTAREGAGLVVASGVIYCLGGYDGLNILNSVEKYDPHTGHWTNVT
          DGSRRHTSMERYDPNIDQWSMLGDMQTAREGAGLVVASGVI.CLGGYDGLNILNSVEKYDPHTGHWTNVT
Retrocopy DGSRRHTSMERYDPNIDQWSMLGDMQTAREGAGLVVASGVIHCLGGYDGLNILNSVEKYDPHTGHWTNVT

Parental  PMATKRSGAGVALLNDHIYVVGGFDGTAHLSSVEAYNIRTDSWTTVTSMTTPRCYVGATVLRGRLYAIAG
          PMATKRSGAGVALLND.IYVVG.FDGTAHLSSVEAYNIRTDS.TT.TSMTTPRCYVGATVLRGRLYAIAG
Retrocopy PMATKRSGAGVALLNDRIYVVGRFDGTAHLSSVEAYNIRTDSRTTATSMTTPRCYVGATVLRGRLYAIAG

Parental  YDGNSLLSSIECYDPIIDSWEVVTSMGTQRCDAGVCVLREK
          Y.G.SLLSSIECY.PIIDSWEVVTSMGTQRCDAGVCVL..K
Retrocopy YEGKSLLSSIECYNPIIDSWEVVTSMGTQRCDAGVCVLHKK

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	0.64 RPM	49.21 RPM
SRP007412_cerebellum	1.25 RPM	59.19 RPM
SRP007412_heart	0.23 RPM	25.42 RPM
SRP007412_kidney	0.60 RPM	62.84 RPM
SRP007412_liver	0.10 RPM	31.52 RPM
SRP007412_testis	0.32 RPM	115.82 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1483 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1483 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1483 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2545

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006231	1 retrocopy	retro_cjac_2151,
Dasypus novemcinctus	ENSDNOG00000010436	1 retrocopy	retro_dnov_2190,
Echinops telfairi	ENSETEG00000007800	2 retrocopies	retro_etel_2103, retro_etel_723,
Homo sapiens	ENSG00000117153	1 retrocopy	retro_hsap_2545,
Macaca mulatta	ENSMMUG00000017849	1 retrocopy	retro_mmul_612,
Nomascus leucogenys	ENSNLEG00000018103	1 retrocopy	retro_nleu_2795,
Otolemur garnettii	ENSOGAG00000014771	1 retrocopy	retro_ogar_1552,
Pongo abelii	ENSPPYG00000000343	1 retrocopy	retro_pabe_1872,
Pan troglodytes	ENSPTRG00000001861	1 retrocopy	retro_ptro_1483 ,
Pan troglodytes	ENSPTRG00000015989	1 retrocopy	retro_ptro_1602,