RetrogeneDB ID: retro_pabe_691

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:51530111..51530779(+)
• 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_691
GGCAAGACAGGGCTGTTCCGAGGTCTGAGCCCCCAACTGATGTGACCCCTCTCCTTTGTAACCGGGGACAGCATGAAGAA
GGTTTTCCCTCCAGATGAAATCAAGCAGGTTTCCAATAAGGATGGATATGAAGACTTCTCTGAAACAAGCAGTGAAGGAG
ACCTCCTAGGAGATGATGATGCAGTGTGTGTCCTGTATGTTGGCCCCCCCCCACTGCATGCCATCTTGATGTGCTGCATG
GTCTAATTTGTGGCATGGGAGGTCAAGTACAGTGGTGTGCTGAGCTCCACTGGGAAGATTTTCAAAGAGGAAGGGCTACT
GGGATTCTTTGTTGGCTTGATCCCTCATGTCCCGGGTGAAGTAGTTTTCTTGTGAGGCTATCACCTGCCGGCCCACTTTA
TCAATGCCTACCTGGTGGATGACAGTGTGAGTGACACCTAGGGGGGCTGAGAAATGACCAGAATCGGGGTTCCCAGTTAG
GCCAGGCCCTGGCCATCTGGAATTACACCAAGTTTGTGATGGAGATCGCAGTGAGCATGCTGACCTACCCTTTCCTGCCA
GTTGGCAGCCTCATGGCTGTGAACAACTGCAGGCCGCAGGCTGGGCTCTCCCCTTACTCCCTGGTGTTCAAATCCTGGAT
TTACTGCTGTAAGTACCTGAGTGTGCAG

Alignment

ORF - retro_pabe_691 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.33 %
• Parental protein coverage: 57.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GKIGLFRGLSPRLMSNALSTVTRGSMKKVFPPDEIEQVSNKD-DMKTSLKKVVKETSYE-MMM-QCVSRM
          GK.GLFRGLSP.LM...LS.VT..SMKKVFPPDEI.QVSNKD.DMKTSLK..VKETS.E.MM...CV...
Retrocopy GKTGLFRGLSPQLM*-PLSFVTGDSMKKVFPPDEIKQVSNKD>DMKTSLKQAVKETS*EMMMQ<VCVLYV

Parental  LAHPLHVISMRCMVQFVGREAKYSGVLSSIGKIFKEEGLLGFFVGLIPHLLGDVVFLWGCNLLAHFINAY
          ....LH.I.M.CMV.FV..E.KYSGVLSS.GKIFKEEGLLGFFVGLIPH..G.VVFL.G..L.AHFINAY
Retrocopy XXXXLHAILMCCMV*FVAWEVKYSGVLSSTGKIFKEEGLLGFFVGLIPHVPGEVVFL*GYHLPAHFINAY

Parental  LVDDSVSDT-PGGLGNDQNPGSQFSQALAIRSYTKFVMGIAVSMLTYPFLLVGDLMAVNNCGLQAGLPPY
          LVDDSVSDT..GGL.NDQN.GSQ..QALAI..YTKFVM.IAVSMLTYPFL.VG.LMAVNNC..QAGL.PY
Retrocopy LVDDSVSDT<LGGLRNDQNRGSQLGQALAIWNYTKFVMEIAVSMLTYPFLPVGSLMAVNNCRPQAGLSPY

Parental  SPVFKSWIHCWKYLSVQ
          S.VFKSWI.C.KYLSVQ
Retrocopy SLVFKSWIYCCKYLSVQ

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	0.17 RPM	361.21 RPM
SRP007412_cerebellum	0.61 RPM	137.41 RPM
SRP007412_heart	0.09 RPM	48.98 RPM
SRP007412_kidney	0.46 RPM	123.74 RPM
SRP007412_liver	0.15 RPM	52.08 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_691 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_691 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_691 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1060

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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,