RetrogeneDB ID: retro_pabe_3011

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:141401798..141402544(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH1
• Ensembl ID: ENSPPYG00000016557
• Aliases: None
• Description: mitochondrial carrier 1 [Source:HGNC Symbol;Acc:17586]

Sequence

>retro_pabe_3011
GGGAGGAAGGTCCTCTATCTGCCAAGCTTCTTCACCTACGCCAAATACGTTGTGCAAGTGGATGGTAAGATAGGGCTGTT
CCGAGGTCTGAGGCCCCAGCTGATGTCCAATGCCCTCTTCACTGTGACCCGGGTAGCATGAAGAAGGCTTTCCCTCTAGA
TGAGATCTAGCAGGTTTCCAACAAGGGTGATATGAAGACTTCCCTGAAGAAAGTTGTGAAGGAGACCTTCTATGGGATAA
TGATGCAGTGCGTGTCCCGCATGTTGGCCCACCCCCTGCATGTCATCTCAATGCGCTGGATGGTCCAGTTTGTGGGATGG
GAAGCCAAGGACAGTGGCGTGCTGAGCTCCATTGGGAAGCTTTTCAAAGAGGAAGGGCTGCTGGGATTTGTTGGATTAAT
CCCTCACCTCCTGGGTGATGTTGTTTTCTCGTGAGGCTGTAACCTACTGGCCCACTTCATCAGTGCCTACCTGGTGGATG
ACAGCTTCCACCAGGCCCTGGCCATCCAGAGCCACACCAAGTGCTTGACAGGGATCACAGTGAGCATGCTGACCTACCCC
TTCCTGCTAGTTGGCGACCTCATGGCTGTGAACAACTGTGGGCTGCAGGCTGGGCTCCCCCGTTACTCCCCGGTGTTCAA
ATCCTGGATTCACTGCTGGAAGTACCTGAGTATGCAGGGCCAGCTCTTCCGAGGCTCCAGCCTGCTTTTCTGCTGGGTGT
CATCAGGATCATGCTTCGCCCTGGAG

Alignment

ORF - retro_pabe_3011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 67.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRKVLYLPSFFTYAKYIVQVDGKIGLFRGLSPRLMSNALSTVTR-GSMKKVFPPDEIEQVSNKDDMKTSL
          GRKVLYLPSFFTYAKY.VQVDGKIGLFRGL.P.LMSNAL.TVTR.GSMKK.FP.DEI.QVSNK.DMKTSL
Retrocopy GRKVLYLPSFFTYAKYVVQVDGKIGLFRGLRPQLMSNALFTVTR<GSMKKAFPLDEI*QVSNKGDMKTSL

Parental  KKVVKETSYEMMMQCVSRMLAHPLHVISMRCMVQFVGREAKYSGVLSSIGKIFKEEGLLGFFVGLIPHLL
          KKVVKET.Y..MMQCVSRMLAHPLHVISMR.MVQFVG.EAK.SGVLSSIGK.FKEEGLLGF.VGLIPHLL
Retrocopy KKVVKETFYGIMMQCVSRMLAHPLHVISMRWMVQFVGWEAKDSGVLSSIGKLFKEEGLLGF-VGLIPHLL

Parental  GDVVFLWGCNLLAHFINAYLVDDSFSQALAIRSYTKFVMGIAVSMLTYPFLLVGDLMAVNNCGLQAGLPP
          GDVVF..GCNLLAHFI.AYLVDDSF.QALAI.S.TK...GI.VSMLTYPFLLVGDLMAVNNCGLQAGLP.
Retrocopy GDVVFS*GCNLLAHFISAYLVDDSFHQALAIQSHTKCLTGITVSMLTYPFLLVGDLMAVNNCGLQAGLPR

Parental  YSPVFKSWIHCWKYLSVQGQLFRGSSLLFRRVSSGSCFALE
          YSPVFKSWIHCWKYLS.QGQLFRGSSLLF..VSSGSCFALE
Retrocopy YSPVFKSWIHCWKYLSMQGQLFRGSSLLFCWVSSGSCFALE

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	361.21 RPM
SRP007412_cerebellum	0.00 RPM	137.41 RPM
SRP007412_heart	0.03 RPM	48.98 RPM
SRP007412_kidney	0.07 RPM	123.74 RPM
SRP007412_liver	0.06 RPM	52.08 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3011 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3011 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3671
Pan troglodytes	retro_ptro_2490
Gorilla gorilla	retro_ggor_2481
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,
Macaca mulatta	ENSMMUG00000021976	1 retrocopy	retro_mmul_1060,
Nomascus leucogenys	ENSNLEG00000010899	1 retrocopy	retro_nleu_423,
Pongo abelii	ENSPPYG00000003296	3 retrocopies	retro_pabe_1392, retro_pabe_1894, retro_pabe_872,
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,