RetrogeneDB ID: retro_ggor_1830

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:22055850..22056620(+)
• 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_1830
ATGTGTCTCTCCTCCTCCCCACCTCGTGGCTGGCAGCAGCCCTCCAGCTTTGGCTCCGTGGACTGGCTCTGCCTGAGCAG
CTGCTCAGGGTCGATCCACACCCCCAGGCCTGCCGATGTCTCCCCCGGGAGCCTCCCTGGCCCGGGCCAGACATTCGGCA
CCCGGGAGCCCCCTCAGGCTGTCAGTACCAAGGAGGCTAGCTCGTCAAATCTGCATGCGCCGGAGAGGGCTGTGGCTGGG
TTGAGTAAGGAGCCAAATCCCTAGCTGGCTCCCGGTGTCCGCATAGCCTTCACCACGGAGCAGGTCCGTGCCTTGGAGGG
CGTCTTCCGGCACCACCAGTACCTGGACCCTCTGGAGCGGAATTGGCTGGCCAGGGAGATGCAGCTCTCAGAGGTCCAGA
TAAAAACCTGGTTTCAAAATCGCCGGATGAAACACAAACGGCAAATGCAGGACTCCCAGCTAAACGGCCCCTTATCGGGG
TCTCTCCACGGGCCCCCTGCTTTCCACTCACCATCTTCTGGCCTTGCCAATGGCCTGCAGCTGCTGTGCCGTTGGGCACC
CCTGCCTGGGCCCCCTGGCTGCCCCTTGGCTCCTTCTGGGGTCTCTGACAAATGGATCAAGAGGCCCTGGCCTCTTCGTG
GGCTTCCTGCTGCGGGCAGCCTCTGGTGTACCACCCCCCACGCCCAGGAAGTGGTGCGCATAAGCTGGGACCAGCCCTGT
CCACGGGGCCCTGGGGCCTGTGTGCTCTGCCAGAGACAGGGGATGCATTT

Alignment

ORF - retro_ggor_1830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLSSSPPRGRQQLSSFGSVDWLSQSSCSGPTHTPRPADFSLGSLPGPGQTSGAREPPQAVSIKEAARSS
          M.LSSSPPRG.QQ.SSFGSVDWL..SSCSG..HTPRPAD.S.GSLPGPGQT.G.REPPQAVS.KEA..SS
Retrocopy MCLSSSPPRGWQQPSSFGSVDWLCLSSCSGSIHTPRPADVSPGSLPGPGQTFGTREPPQAVSTKEAS-SS

Parental  NLPAPERTVAGLSKEPNTLRAPRVRTAFTMEQVRTLEGVFQHHQYLSPLERKRLAREMQLSEVQIKTWFQ
          NL.APER.VAGLSKEPN...AP.VR.AFT.EQVR.LEGVF.HHQYL.PLER..LAREMQLSEVQIKTWFQ
Retrocopy NLHAPERAVAGLSKEPNP*LAPGVRIAFTTEQVRALEGVFRHHQYLDPLERNWLAREMQLSEVQIKTWFQ

Parental  NRRMKHKRQMQDPQLHSPFSGSLHAPPAFYSPSSGLPNGLQLLCSWAPLPRPQ-ALMLPPGSFWGLCRVG
          NRRMKHKRQMQD.QL..P.SGSLH.PPAF.SPSSGL.NGLQLLC.WA..P.P..A..LP.GSFWGL....
Retrocopy NRRMKHKRQMQDSQLNGPLSGSLHGPPAFHSPSSGLANGLQLLCRWA--PLPG<APWLPLGSFWGL*QMD

Parental  QEALASAWASCYGQPLAYHPPSPGSGVHPLGPALSTG-LGLCALLETRDAF
          QEALAS.WASC.GQPL.YHPP.PGSG.H.LGPALSTG..GLCAL.ET.DAF
Retrocopy QEALASSWASCCGQPLVYHPPRPGSGAHKLGPALSTGPWGLCALPETGDAF

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	0.00 RPM	0.05 RPM
SRP007412_cerebellum	0.04 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_1830 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1830 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2612
Pan troglodytes	retro_ptro_1761
Macaca mulatta	retro_mmul_1477

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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,