RetrogeneDB ID: retro_ptro_2745

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:45154586..45155682(-)
• Located in intron of: ENSPTRG00000020227

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSFL1C
• Ensembl ID: ENSPTRG00000013164
• Aliases: None
• Description: None

Sequence

>retro_ptro_2745
GCAGCGGAGCAACAGAAGTCGCTGAGAGAGTTCGTGGGGGTGATGGGCACCGAGCAGGACCGGGCCTGCTTCTTCCTCAA
GTCGGCTACCTGGGACTTGCAGATTGCGCTAGCGAGCTTTTATGAGGACAGAGGGGAAGACATCATAACCATTTCACAGG
CAACCCCCAGTTCAGTGTCCAGAGGCACAGCCCCTAGTGATAATAGAGTGACATCCTTTAGAGATCTCACTCATGACCAA
GATGAGGATGAGGAAGAGGAGGAAGGCCAGAGGTTTTATGCTGGGGCCTCAGAGAGAAGTGGACAGCAGATTGTTGGCCC
TCCCAGAAAGAAGAGTTCCAATGAGCTGGTGGATGATCTCTTTAAAGGTGCCAAAGAGCATGGAGCTGTAGCTGTGGAGC
GAGTGACCAACAGACCTGGAGAGACCAGTACACCAAGACCATTTGCCGGAGATGGCTATGGCCTTGGGGCAGCACCAGAG
GAAGAGTCTGCTTATGTGGCAGGAGAAAAGAGACATCATTCCAGCCAAGATGTTCATGTAGTACTGAAACTCTGCAAGAG
TGGATTCAGCCTGGATAATGGAGAACTCAGAAGCTACTGAGACCCATCTGATGCCCAGTTTCTGGAGTCTATCCACAGAA
GGGAGGTGCCAGCAGAGCTGTGGAGGCTAGCTCACAGTGGACAGGCGAACTTGGATATGGAGGACCATCAGGACGAGGAC
TTTATGAAGTCCAAATAAGCCTTCAAAGCCCTTCACTGGCGACGGTCAGACACCGAGCAGCACTGCCCCCTAGGTGTTGA
GTACCATCTCTCCAGTCCAACTGGCAGAAAATGAAGTCAAAGCCAACTCTTCCATCTTAATCGTCAAATCAGAGACTACC
ACAAACATCCAAATTCGGCTTGCAGACGGTGGGAGGCTGGTGCAGAAATTTAACCACAGCCACAGGATCAGCAACATCCA
ACTCTTCATTGTGGATGCCCAGCCAGCCATGGCTGCCACCAGCTTTATCCTCATGACTACTTTCCCAAACAAAGAGCTGG
CTGACGAGAGCTGGACCCTGAAGGAAGCCAACCTGCTCAATGCTGCCATCATGCAG

Alignment

ORF - retro_ptro_2745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.29 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAERQEALREFVAVTGAEEDRARFFLESAGWDLQIALASFYEDGGDEDIVTISQATPSSVSRGTAPSDNR
          AAE.Q..LREFV.V.G.E.DRA.FFL.SA.WDLQIALASFYED.G.EDI.TISQATPSSVSRGTAPSDNR
Retrocopy AAEQQKSLREFVGVMGTEQDRACFFLKSATWDLQIALASFYEDRG-EDIITISQATPSSVSRGTAPSDNR

Parental  VTSFRDLIHDQDEDEEEEEGQRFYAGGSERSGQQIVGPPRKKSPNELVDDLFKGAKEHGAVAVERVTKSP
          VTSFRDL.HDQDEDEEEEEGQRFYAG.SERSGQQIVGPPRKKS.NELVDDLFKGAKEHGAVAVERVT..P
Retrocopy VTSFRDLTHDQDEDEEEEEGQRFYAGASERSGQQIVGPPRKKSSNELVDDLFKGAKEHGAVAVERVTNRP

Parental  GETSKPRPFAGGGYRLGAAPEEESAYVAGEKRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLE
          GETS.PRPFAG.GY.LGAAPEEESAYVAGEKR.HSSQDVHVVLKL.KSGFSLDNGELRSY.DPS.AQFLE
Retrocopy GETSTPRPFAGDGYGLGAAPEEESAYVAGEKRHHSSQDVHVVLKLCKSGFSLDNGELRSY*DPSDAQFLE

Parental  SIRRGEVPAELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKA-FTGEGQKLGSTAPQVLSTSSPAQQAENE
          SI.R.EVPAEL.RLAH.GQ.NLDMEDH.DEDF.K.K.AFKA.FTG.GQ...STAP.VLST.SP.Q.AENE
Retrocopy SIHRREVPAELWRLAHSGQANLDMEDHQDEDFMKSK*AFKA>FTGDGQTPSSTAP*VLSTISPVQLAENE

Parental  AKASSSILIDESEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFILMTTFPNKELAD
          .KA.SSILI..SE.TTNIQIRLADGGRLVQKFNHSHRIS.I.LFIVDA.PAMAATSFILMTTFPNKELAD
Retrocopy VKANSSILIVKSETTTNIQIRLADGGRLVQKFNHSHRISNIQLFIVDAQPAMAATSFILMTTFPNKELAD

Parental  ESQTLKEANLLNAVIVQ
          ES.TLKEANLLNA.I.Q
Retrocopy ESWTLKEANLLNAAIMQ

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	0.07 RPM	67.92 RPM
SRP007412_cerebellum	0.11 RPM	64.89 RPM
SRP007412_heart	0.44 RPM	45.29 RPM
SRP007412_kidney	1.49 RPM	52.51 RPM
SRP007412_liver	0.69 RPM	84.29 RPM
SRP007412_testis	0.11 RPM	55.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2745 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2745 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2745 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2718

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000088833	1 retrocopy	retro_hsap_4050,
Gorilla gorilla	ENSGGOG00000013539	1 retrocopy	retro_ggor_2718,
Macropus eugenii	ENSMEUG00000003940	2 retrocopies	retro_meug_1890, retro_meug_605,
Macaca mulatta	ENSMMUG00000015994	1 retrocopy	retro_mmul_2337,
Mus musculus	ENSMUSG00000027455	1 retrocopy	retro_mmus_2565,
Nomascus leucogenys	ENSNLEG00000009341	1 retrocopy	retro_nleu_2800,
Otolemur garnettii	ENSOGAG00000002630	2 retrocopies	retro_ogar_1144, retro_ogar_1609,
Pongo abelii	ENSPPYG00000010851	1 retrocopy	retro_pabe_3324,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Pan troglodytes	ENSPTRG00000013164	1 retrocopy	retro_ptro_2745 ,
Pan troglodytes	ENSPTRG00000033886	1 retrocopy	retro_ptro_2668,