RetrogeneDB ID: retro_ptro_414

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:24544390..24545301(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP35
• Ensembl ID: ENSPTRG00000012711
• Aliases: None
• Description: None

Sequence

>retro_ptro_414
ATGGCAGCCTTTGCCATGGAACTCCAGGTGCCTGCATTAGGATCTGAACCAATGATGCTGGCTTCATCTCCAAAGCCAGG
AGTTAATGCCCAGTTCTTACCTGGATTTTGAATGCGGAATTTGCCAGCCCTGGTGACTCCACAATCTCGATCAATTAGTG
GCCCTTCAGTAGGAGTAGTGGAAATGAGATCACCTTTACTTGCAGGTGGGTCACCACCACAACCAGTTGTACTAGCTCAT
AAAGATAAAAGTGGCGCTCCACAAGTTAGAAGTATATATGATGACATTTCTAGCCTGGGATTTGGATCAACACCTTTAAC
TTCAAGAAGACAGCCAAACATTTCATGATGCAGAGTCCTCTTACTGGAGTTACATCTACTCCTGGAACAGGGCAAAGTAC
GTTTAGTCCAGCAAATGTCGGTCAGTCATGAAAGATGACATTTTCTCCTTCCCGGTTGGATCCTTTTTATACTCAAGGAG
ATTCTTTGACTTCAGAAGGTCACCTTGATGACACTTGGGTGACTGTGTTTGGGTTTTCTCAAGCCTCTGCTTCCTACATA
TTATTACAATTTGCACAGTATGGGAATATCTTAAAACACATGATGTCTAACACAGGAAATTGAATGTATATTCATTATCA
GTCTAAACTGCAGGCTCGGAAAGCCTTAACCAAAGATGGGAGGATTTTTAGAGAATTCATCATGATTGGTGTAAAACCCT
GTATTGACTAAACTGTAATGGGAAGCACTGACCGACGTGCTTTATCATCTCCATCTTTTGCCTTTACACCACCAATCAAA
ACTTTAGGTACACTAGCACAACCTGAAAGTACTCCTAGGATTTCTGCCATGAGACCTCTTGCTACAGCATACAAAGATTC
TACTAGTGATTATCAGGTTATTTCTGACAGA

Alignment

ORF - retro_ptro_414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.04 %
• Parental protein coverage: 93.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAFAVEPQGPALGSEPMMLGSPTSPKPGVNAQFLPGFLMGDLPAPVTPQPRSISGPSVGVMEMRSPLLA
          MAAFA.E.Q.PALGSEPMML.S..SPKPGVNAQFLPGF.M..LPA.VTPQ.RSISGPSVGV.EMRSPLLA
Retrocopy MAAFAMELQVPALGSEPMMLAS--SPKPGVNAQFLPGF*MRNLPALVTPQSRSISGPSVGVVEMRSPLLA

Parental  GGSPPQPVVPAHKDKSGAPPVRSIYDDISSPGLGSTPLTSRRQPNIS-VMQSPLVGVTSTPGTGQSMFSP
          GGSPPQPVV.AHKDKSGAP.VRSIYDDISS.G.GSTPLTSRRQPNIS..MQSPL.GVTSTPGTGQS.FSP
Retrocopy GGSPPQPVVLAHKDKSGAPQVRSIYDDISSLGFGSTPLTSRRQPNIS<MMQSPLTGVTSTPGTGQSTFSP

Parental  ASIGQPRKTTLSPAQLDPFYTQGDSLTSEDHLDDSWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGN
          A..GQ..K.T.SP..LDPFYTQGDSLTSE.HLDD.WVTVFGF.QASASYILLQFAQYGNILKH.MSNTGN
Retrocopy ANVGQS*KMTFSPSRLDPFYTQGDSLTSEGHLDDTWVTVFGFSQASASYILLQFAQYGNILKHMMSNTGN

Parental  WMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKSVMESSDRCALSSPSLAFTPPIKTLGTPTQPGS
          .M.I.YQSKLQARKAL.KDGRIF.E.IMIGVKPCID..VM.S.DR.ALSSPS.AFTPPIKTLGT..QP.S
Retrocopy *MYIHYQSKLQARKALTKDGRIFREFIMIGVKPCID*TVMGSTDRRALSSPSFAFTPPIKTLGTLAQPES

Parental  TPRISTMRPLATAYKASTSDYQVISDR
          TPRIS.MRPLATAYK.STSDYQVISDR
Retrocopy TPRISAMRPLATAYKDSTSDYQVISDR

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	0.02 RPM	4.22 RPM
SRP007412_cerebellum	0.00 RPM	5.81 RPM
SRP007412_heart	0.03 RPM	2.65 RPM
SRP007412_kidney	0.05 RPM	7.43 RPM
SRP007412_liver	0.00 RPM	4.35 RPM
SRP007412_testis	0.00 RPM	22.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_414 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_414 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_551
Pongo abelii	retro_pabe_508
Macaca mulatta	retro_mmul_2387

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008469	1 retrocopy	retro_eeur_666,
Homo sapiens	ENSG00000163002	1 retrocopy	retro_hsap_551,
Gorilla gorilla	ENSGGOG00000009919	1 retrocopy	retro_ggor_500,
Macaca mulatta	ENSMMUG00000004140	1 retrocopy	retro_mmul_2387,
Nomascus leucogenys	ENSNLEG00000006423	1 retrocopy	retro_nleu_2019,
Pongo abelii	ENSPPYG00000012998	1 retrocopy	retro_pabe_508,
Pan troglodytes	ENSPTRG00000012711	1 retrocopy	retro_ptro_414 ,
Ictidomys tridecemlineatus	ENSSTOG00000000711	2 retrocopies	retro_itri_755, retro_itri_760,