RetrogeneDB ID: retro_ggor_2708

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:33827624..33828340(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VENTX
• Ensembl ID: ENSGGOG00000003340
• Aliases: None
• Description: None

Sequence

>retro_ggor_2708
TTTGGCTCCGTGGGCTGGCTCTCCCAGAACAGCTGCTCAGGGCCGACCCACACCCCCAGGCCTGCCGACGTCTCCCCGGG
GAGCCACCCTGGCCCGGGCCAGACATCCGGCACCCGGGAGCCCCCTCAGGCCGTCAGCGTCAAGAAGGCTCGGTCCTCAA
ATCTGCCTGCGCCGGAGAGGGCCGTGGCTGGGTTGGGTAAGAAGCCAAACCCCTGGCAGGCCCCCTGTGTAGGCACAGCC
TTCACCACCGAGCAGGTCCGCGCCTTGGAGGGCGTCTTCCAGCACCACCAGGACCTGGGCCCTCTGGAACGGAAAAGGCT
GGCAGGGAGATGCAGCTCTCGGACGTCCAGACAAAAACCTGGTTTCAAAACCGCCAGATGAAACAGAAACGGCAAACGCA
GGACTCCCAGCTGAACAGCCCCTTCTCTGTGTCTCTCCACGCGCCCCCTGCTTTCCACTCACCGTCTTCTGGCCTTGTCA
ATGACCTGCAGCTGCCGTGCCCTTGGGCACCCCTGCCAGGGCCCCAGGCTCTGATGCTGCCCCCTGGCTCTCTCTGGGGT
ATCTGCCAAGTGGAACAAGAGGCCCTGGCCTCTGCGGGGGCTTCCTGCTATGGGCAGCCTCTGGCGTACCACCGGCCAAG
CCCAGGAAGTGGCGTGCGTACGCTGGGACCAGCTCTGTCCACGGGGCCCTGGGGCCTGAGCGCGCTGCAGGAGACG

Alignment

ORF - retro_ggor_2708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 92.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FGSVDWLSQSSCSGPTHTPRPADFSLGSLPGPGQTSGAREPPQAVSIKEAARSSNLPAPERTVAGLSKEP
          FGSV.WLSQ.SCSGPTHTPRPAD.S.GS.PGPGQTSG.REPPQAVS.K.A.RSSNLPAPER.VAGL.K.P
Retrocopy FGSVGWLSQNSCSGPTHTPRPADVSPGSHPGPGQTSGTREPPQAVSVKKA-RSSNLPAPERAVAGLGKKP

Parental  NTLRAPRVRTAFTMEQVRTLEGVFQHHQYLSPLERKRLA-REMQLSEVQIKTWFQNRRMKHKRQMQDPQL
          N...AP.V.TAFT.EQVR.LEGVFQHHQ.L.PLERKRLA.REMQLS.VQ.KTWFQNR.MK.KRQ.QD.QL
Retrocopy NPWQAPCVGTAFTTEQVRALEGVFQHHQDLGPLERKRLA<REMQLSDVQTKTWFQNRQMKQKRQTQDSQL

Parental  HSPFSGSLHAPPAFYSPSSGLPNGLQLLCSWAPLPRPQALMLPPGSFWGLCRVGQEALASAWASCYGQPL
          .SPFS.SLHAPPAF.SPSSGL.N.LQL.C.WAPLP.PQALMLPPGS.WG.C.V.QEALASA.ASCYGQPL
Retrocopy NSPFSVSLHAPPAFHSPSSGLVNDLQLPCPWAPLPGPQALMLPPGSLWGICQVEQEALASAGASCYGQPL

Parental  AYHPPSPGSGVHPLGPALSTG-LGLCALLET
          AYH.PSPGSGV..LGPALSTG..GL.AL.ET
Retrocopy AYHRPSPGSGVRTLGPALSTGPWGLSALQET

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	0.05 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.16 RPM
SRP007412_kidney	0.00 RPM	0.20 RPM
SRP007412_liver	0.00 RPM	0.53 RPM
SRP007412_testis	0.00 RPM	0.21 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_2708 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2708 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4038
Pan troglodytes	retro_ptro_2736

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151650	4 retrocopies	retro_hsap_1027, retro_hsap_2612, retro_hsap_3973, retro_hsap_4038,
Gorilla gorilla	ENSGGOG00000003340	3 retrocopies	retro_ggor_1830, retro_ggor_2668, retro_ggor_2708 ,
Macaca mulatta	ENSMMUG00000000543	2 retrocopies	retro_mmul_1477, retro_mmul_2294,
Nomascus leucogenys	ENSNLEG00000002047	5 retrocopies	retro_nleu_2033, retro_nleu_2054, retro_nleu_635, retro_nleu_664, retro_nleu_905,
Pan troglodytes	ENSPTRG00000003087	4 retrocopies	retro_ptro_1761, retro_ptro_2698, retro_ptro_2736, retro_ptro_702,