RetrogeneDB ID: retro_pabe_3287

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:115549948..115550357(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT10B
• Ensembl ID: ENSPPYG00000019056
• Aliases: None
• Description: tRNA methyltransferase 10 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:26454]

Sequence

>retro_pabe_3287
TGTGTGAAGAGCGAAGATGAATTTTCTAGCGACTTGCTAGACATAAAAGAAGACTTCTTTTAGTTTATTTCCTCTGGAAA
CCCTTGTGTTCCTGACTCCTGACTCAGAATACACTATTGAAGATGTTGATCTAAACAAAGTTTGTATCTTTGATGGACTT
GTGGATGAAAGCATTCAGAAGAAGGTGACATTTCAAAAGGCCCAGGAATACTCTTTCAGGACAGCCCACTTGTCTGTCAT
TCCAGGGATACATGATCAGACACCAGAGTACAAATAACTCTCATTTAGGGATGCTGGCCATCAATCAAGTATTTGATATT
CTGTCCACTTATTTTGAGACTCTTAACTGGCCTGAAGCATTGAAGACGGGAATTTCTTCCAGAAAAGTTATATTCTTCAG
AGCACAGTG

Alignment

ORF - retro_pabe_3287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CVRMNDGFSSYLLDITEED-CFSLFPLETLVYLTPDSEHALEDVDLNKVYILGGLVDESIQKKVT-FQKA
          CV...D.FSS.LLDI..ED..FSLFPLETLV.LTPDSE...EDVDLNKV.I..GLVDESIQKKVT.F...
Retrocopy CVKSEDEFSSDLLDI-KED>SFSLFPLETLVFLTPDSEYTIEDVDLNKVCIFDGLVDESIQKKVT>FKRP

Parental  RE-YSVKTARLPIQEYMVRNQNGKNYHSEILAINQVFDILSTYLETHNWPEALKKGVSS-GKGYILRNSV
          R...S.....L..Q.YM.R.Q...N.H...LAINQVFDILSTY.ET.NWPEALK.G.SS..K.YIL...V
Retrocopy RNTLSGQPTCLSFQGYMIRHQSTNNSHLGMLAINQVFDILSTYFETLNWPEALKTGISS<QKSYILQSTV

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	8.02 RPM
SRP007412_cerebellum	0.00 RPM	17.39 RPM
SRP007412_heart	0.00 RPM	2.53 RPM
SRP007412_kidney	0.00 RPM	8.42 RPM
SRP007412_liver	0.00 RPM	5.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3287 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3287 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000010994	1 retrocopy	retro_ocun_671,
Pongo abelii	ENSPPYG00000019056	1 retrocopy	retro_pabe_3287 ,