RetrogeneDB ID: retro_ggor_2481

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:139447855..139448433(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH1
• Ensembl ID: ENSGGOG00000003908
• Aliases: None
• Description: None

Sequence

>retro_ggor_2481
CGGCTGATGTCCGACGCCCTCTTCACTGTGACCCGGGTAGCATGAAGAAGGCTTTCCCTCTAGATGAGATCTAGCAGGTT
TCCAACAAGGGTGATATGAAGACTTCCCTGAAGAAAGTTGTGAAGGAGACCTCCTATGGGATAATGATGCAGTGCGTGTC
CCGCATGTTGACCCACCCCGTGTATGTCATCTCAATGTGCTGGATGGTCCAGTTTGTGGAATGGGAAGCCAAGGACAGTG
GCGTGCTGAGCTCCATTGGGAAGCTTTTCAAAGAGGAAGGGCTGCTGGGATTTGTTGGATTAATCCCTCACCTCCTGGGT
GATGTGGTTTTCTTGTGAGGCTGTAACCTACTGGCCTACTTCATCAGTGCCTACCTGGTGGATGACAGCCTCCACCAGGC
CCTGGCCATCCGGAGCCACACCAAATGCTTGACAGGGATTGCAGTGAGCATGCTGACCTACCCCTTCCTGCTAGTCGGCG
ACCTCATGGCTGTGAACAACTGTGGGCTGCAGGCTGGGCTCCCCCATTACTCCCCGGTGTTCAAATCCTGGATTCACTGC
TGGAAGTAGCTGAGTATG

Alignment

ORF - retro_ggor_2481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.1 %
• Parental protein coverage: 52.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLMSNALSTVTR-GSMKKVFPPDEIEQVSNKDDMKTSLKKVVKETSYEMMMQCVSRMLAHPLHVISMRCM
          RLMS.AL.TVTR.GSMKK.FP.DEI.QVSNK.DMKTSLKKVVKETSY..MMQCVSRML.HP..VISM..M
Retrocopy RLMSDALFTVTR<GSMKKAFPLDEI*QVSNKGDMKTSLKKVVKETSYGIMMQCVSRMLTHPVYVISMCWM

Parental  VQFVGREAKYSGVLSSIGKIFKEEGLLGFFVGLIPHLLGDVVFLWGCNLLAHFINAYLVDDSFSQALAIR
          VQFV..EAK.SGVLSSIGK.FKEEGLLGF.VGLIPHLLGDVVFL.GCNLLA.FI.AYLVDDS..QALAIR
Retrocopy VQFVEWEAKDSGVLSSIGKLFKEEGLLGF-VGLIPHLLGDVVFL*GCNLLAYFISAYLVDDSLHQALAIR

Parental  SYTKFVMGIAVSMLTYPFLLVGDLMAVNNCGLQAGLPPYSPVFKSWIHCWKYLSV
          S.TK...GIAVSMLTYPFLLVGDLMAVNNCGLQAGLP.YSPVFKSWIHCWK.LS.
Retrocopy SHTKCLTGIAVSMLTYPFLLVGDLMAVNNCGLQAGLPHYSPVFKSWIHCWK*LSM

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	417.82 RPM
SRP007412_cerebellum	0.00 RPM	151.45 RPM
SRP007412_heart	0.00 RPM	65.42 RPM
SRP007412_kidney	0.00 RPM	106.27 RPM
SRP007412_liver	0.03 RPM	58.03 RPM
SRP007412_testis	0.00 RPM	112.20 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_2481 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2481 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3671
Pan troglodytes	retro_ptro_2490
Pongo abelii	retro_pabe_3011
Callithrix jacchus	retro_cjac_2480

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000137409	2 retrocopies	retro_hsap_3671, retro_hsap_856,
Gorilla gorilla	ENSGGOG00000003908	1 retrocopy	retro_ggor_2481 ,
Gorilla gorilla	ENSGGOG00000008281	3 retrocopies	retro_ggor_1267, retro_ggor_3083, retro_ggor_822,
Macaca mulatta	ENSMMUG00000021976	1 retrocopy	retro_mmul_1060,
Nomascus leucogenys	ENSNLEG00000010899	1 retrocopy	retro_nleu_423,
Pongo abelii	ENSPPYG00000016557	2 retrocopies	retro_pabe_3011, retro_pabe_691,
Pan troglodytes	ENSPTRG00000018115	1 retrocopy	retro_ptro_2490,
Tarsius syrichta	ENSTSYG00000014777	1 retrocopy	retro_tsyr_488,
Tursiops truncatus	ENSTTRG00000001966	2 retrocopies	retro_ttru_1101, retro_ttru_563,