RetrogeneDB ID: retro_ggor_500

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:27311620..27312531(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP35
• Ensembl ID: ENSGGOG00000009919
• Aliases: None
• Description: None

Sequence

>retro_ggor_500
GTGGCAGCCTTTGCCATGGAACTCCAGGTGCCTGCGTTAGGATCTGAACCAATGATGCTGGCTTCATCTCCAAAGCCAGG
AGTTAATGCCCAGTTCTTACCTGGATTTTGAATGTGGAATTTGCCAGCCCTGGTGACTCCACAATCTTGATCAATTAGTG
GCCCTTCAGTAGGAGTAGTGGAAATGAGATCACCTTTACTTGCAGGTGGGTCACCACCACAACCAGTTGTACTAGCTCAT
AAAGATAAAAGTGGCGCTCCACAAGTTAGAAGTATATATGATGACATTTCTAGCCTGGGATTTGGATCAACACCTTTAAC
TTCAAGAAGACAGCCAAACATTTCATGATGCAGAGTCCTCTTACTGGAGTTACATCTACTCCTGGAACAGGGCAAAGTAT
GTTTAGTCCAGCAAATGTCGGTCAGTCATGAAAGATGACGTTTTCTCCTTCCCAGTTGGATCCTTTTTATACTCAGGGAG
ATTCTTTGACTTCAGAAGATCACCTTGATGACACTTGGGTGACTGTGTTTGGGTTTTCTCAAGCCTCTGCTTCCTACATA
TTATTACAATTTGCACAGTATGGGAATATCTTAAAACACATGATGTCTAACACAGGAAATTGAATGTATATTCATTATCA
GTCTAAACTACAGGCTCAGAAAGCCTTAACCAAAGATGGGAGGATTTTTAGAGAATTCATCATGATTGGTGTAAAACCCT
GTATTGACTAAAGTGTAATGGGAAGCACTGACAGACGTGCTTTATCATCTCCATCTTTCGCCTTTACACCACCAATCAAA
ACTTTAGGTACACTAGCACAACCTGAAAGTACTCCTAGGACTTCTGCCATGAGACCTCTTGCTACAGCATACAAAGATTC
TACTAGTGATTATCAGGTTATTTCTGACAGA

Alignment

ORF - retro_ggor_500 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: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAFAVEPQGPALGSEPMMLGSPTSPKPGVNAQFLPGFLMGDLPAPVTPQPRSISGPSVGVMEMRSPLLA
          .AAFA.E.Q.PALGSEPMML.S..SPKPGVNAQFLPGF.M..LPA.VTPQ..SISGPSVGV.EMRSPLLA
Retrocopy VAAFAMELQVPALGSEPMMLAS--SPKPGVNAQFLPGF*MWNLPALVTPQS*SISGPSVGVVEMRSPLLA

Parental  GGSPPQPVVPAHKDKSGAPPVRSIYDDISSPGLGSTPLTSRRQPNIS-VMQSPLVGVTSTPGTGQSMFSP
          GGSPPQPVV.AHKDKSGAP.VRSIYDDISS.G.GSTPLTSRRQPNIS..MQSPL.GVTSTPGTGQSMFSP
Retrocopy GGSPPQPVVLAHKDKSGAPQVRSIYDDISSLGFGSTPLTSRRQPNIS<MMQSPLTGVTSTPGTGQSMFSP

Parental  ASIGQPRKTTLSPAQLDPFYTQGDSLTSEDHLDDSWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGN
          A..GQ..K.T.SP.QLDPFYTQGDSLTSEDHLDD.WVTVFGF.QASASYILLQFAQYGNILKH.MSNTGN
Retrocopy ANVGQS*KMTFSPSQLDPFYTQGDSLTSEDHLDDTWVTVFGFSQASASYILLQFAQYGNILKHMMSNTGN

Parental  WMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKSVMESSDRCALSSPSLAFTPPIKTLGTPTQPGS
          .M.I.YQSKLQA.KAL.KDGRIF.E.IMIGVKPCID.SVM.S.DR.ALSSPS.AFTPPIKTLGT..QP.S
Retrocopy *MYIHYQSKLQAQKALTKDGRIFREFIMIGVKPCID*SVMGSTDRRALSSPSFAFTPPIKTLGTLAQPES

Parental  TPRISTMRPLATAYKASTSDYQVISDR
          TPR.S.MRPLATAYK.STSDYQVISDR
Retrocopy TPRTSAMRPLATAYKDSTSDYQVISDR

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	3.93 RPM
SRP007412_cerebellum	0.00 RPM	5.12 RPM
SRP007412_heart	0.00 RPM	1.19 RPM
SRP007412_kidney	0.00 RPM	5.72 RPM
SRP007412_liver	0.05 RPM	6.83 RPM
SRP007412_testis	0.00 RPM	35.33 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_500 has 0 orthologous retrocopies within eutheria group .

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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,