RetrogeneDB ID: retro_ggor_2718

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:45279974..45281073(-)
• Located in intron of: ENSGGOG00000007599

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSFL1C
• Ensembl ID: ENSGGOG00000013539
• Aliases: None
• Description: None

Sequence

>retro_ggor_2718
GCAGTGGAGCAACAGGAGACGCTGAGAGAGTTCGTGGTGGTGATGGGCACCGAGCAGGACCGGGCCTGCTTCTTCCTCGA
GTCGGCTACCTGGGACTTGCAGATTGCGCTAGCGAGCTTTTTATGAGGACAGAGGGGAAGAAGACATCATAACCATTTCA
CAGGCAACCCCCAGTTCAGTGTCCAGAGGCACAGCCCCTAGTGATAATAGAGTGACATCCTTTAGAGATCTCACTCATGA
CCAAGATGAGGATGAGGAAGAGGAGGAAGGCCAGAGGTTTTATGCTGGGGCCTCAGAGAGAAGTGGACAGCAGATTGTTG
GCCCTCCCAGAAAGAAAAGTTCCAATGAGCTGGTGGATGATCTCTTTAAAGGTGCCAAAGAGCATGGAGCTGTAGCTGTG
AAGCGAGTGACCAACAGACCTGGAGAGACCAGTACACCAAGACCATTTGCCGGAGATGGCTATGGACTTGGGGCAGCACC
AGAGGAAGAGTCTGCTTATGTGGCAGGAGAAAAGAGACATCATTCCAGCCAAGATGTTCATGTAGTACTGAAACTCTGCA
AGAGTGGATTCAGCCTGGATAATGGAGAACTCAGAAGCTACTGAGACCCATCCGATGCCCAGTTTCTGGAGTCTATCCAT
GGAAGGGAGGTGCCAGCAGAGCTGTGGAGGCTAGCTCACAGTGGACAGGCAAACTTGGATATGGAGGACCATCAGGACGA
GGACTTTATGAAGTCCAAATAAGCCTTCAAAGCCTTCACTGGCGAGGGTCAGACACCGAGCAGCACTGCCCCCTAGGTGT
TGAGTACCATCTCTCCAGTCCAACTGGCAGAAAATGAAGCCAAAGCCAGCTCTTCCATCTTAATCGTCGAATCAGAGACT
ACCACAAACATCCAAATTCGGCTTGCAGACAGTGGGAGGCTGGTGCAGAAATTTAACCACAGCCACAGGATCAGCAACAT
CCAACTCTTCATCGTGGATGCCCGGCCAGCCATGGCTGCCACCAGGTTTATCCTCATGACTACTTTCCCAAACAAAGAGC
TGGCTGACGAGAGCTGGACCCTGAAGGAAGCCAACCTGCTCAATGCTGCCATCATGCAG

Alignment

ORF - retro_ggor_2718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.37 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAERQEALREFVAVTGAEEDRARFFLESAGWDLQIALASF-YEDGGDEDIVTISQATPSSVSRGTAPSDN
          A.E.QE.LREFV.V.G.E.DRA.FFLESA.WDLQIALASF.YED.G.EDI.TISQATPSSVSRGTAPSDN
Retrocopy AVEQQETLREFVVVMGTEQDRACFFLESATWDLQIALASF>YEDRGEEDIITISQATPSSVSRGTAPSDN

Parental  RVTSFRDLIHDQDEDEEEEEGQRSRFYAGGSERSGQQIVGPPRKKSPNELVDDLFKGAKEHGAVAVERVT
          RVTSFRDL.HDQDEDEEEEEGQR..FYAG.SERSGQQIVGPPRKKS.NELVDDLFKGAKEHGAVAV.RVT
Retrocopy RVTSFRDLTHDQDEDEEEEEGQR--FYAGASERSGQQIVGPPRKKSSNELVDDLFKGAKEHGAVAVKRVT

Parental  KSPGETSKPRPFAGGGYRLGAAPEEESAYVAGEKRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQ
          ..PGETS.PRPFAG.GY.LGAAPEEESAYVAGEKR.HSSQDVHVVLKL.KSGFSLDNGELRSY.DPS.AQ
Retrocopy NRPGETSTPRPFAGDGYGLGAAPEEESAYVAGEKRHHSSQDVHVVLKLCKSGFSLDNGELRSY*DPSDAQ

Parental  FLESIRRGEVPAELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLSTSSPAQQAE
          FLESI...EVPAEL.RLAH.GQ.NLDMEDH.DEDF.K.K.AFKAFTGEGQ...STAP.VLST.SP.Q.AE
Retrocopy FLESIHGREVPAELWRLAHSGQANLDMEDHQDEDFMKSK*AFKAFTGEGQTPSSTAP*VLSTISPVQLAE

Parental  NEAKASSSILIDESEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFILMTTFPNKEL
          NEAKASSSILI.ESE.TTNIQIRLAD.GRLVQKFNHSHRIS.I.LFIVDARPAMAAT.FILMTTFPNKEL
Retrocopy NEAKASSSILIVESETTTNIQIRLADSGRLVQKFNHSHRISNIQLFIVDARPAMAATRFILMTTFPNKEL

Parental  ADESQTLKEANLLNAVIVQ
          ADES.TLKEANLLNA.I.Q
Retrocopy ADESWTLKEANLLNAAIMQ

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	0.43 RPM	89.15 RPM
SRP007412_cerebellum	0.28 RPM	51.41 RPM
SRP007412_heart	0.03 RPM	25.52 RPM
SRP007412_kidney	1.59 RPM	44.12 RPM
SRP007412_liver	0.63 RPM	32.58 RPM
SRP007412_testis	0.93 RPM	48.28 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_2718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2718 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2745

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000088833	1 retrocopy	retro_hsap_4050,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463,
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	ENSPTRG00000013164	1 retrocopy	retro_ptro_2745,