RetrogeneDB ID: retro_pabe_3425

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:76586529..76586897(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TEN1
• Ensembl ID: ENSPPYG00000008646
• Aliases: None
• Description: TEN1 CST complex subunit [Source:HGNC Symbol;Acc:37242]

Sequence

>retro_pabe_3425
GTGATGCTGCCCAAACCTGGGACCTATTCCCTCCACTGGGAGGTCAGTACAAGCCAAGTTCCTGGTGGGGTCACACTGAG
AACATTTGGCAGGTTGTGCCTCTATGACGTGATCAGTCCGGAGTGACGCTGATGGCTCAGCATGGATCTGATCGGCACCA
GGTTCTTGTCTGTACCAAGCTGGTGAAGCCCTTCCAAGCCCAGGTGGGCTCCCTGTACCTTGTCCTCGGGGGGCTCCAGG
ACCAGCAGTAAGGAGGCTCCATGGTAAAGGCACTGGTGCTGAACTGTGTGGAGGGGATGGACCTGCCCTTGTAAGAACAA
GCCAAGCGGGAGCAGAGGCAGTACTAGCGTGTGAGGGACGGCGGCCAG

Alignment

ORF - retro_pabe_3425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMLPKPGTYYLPWEVSAGQVPDGSTLRTFGRLCLYDMI-QSRVTLMAQHGSDQHQVLVCTKLVEPFHAQV
          .MLPKPGTY.L.WEVS..QVP.G.TLRTFGRLCLYD.I.QS.VTLMAQHGSD.HQVLVCTKLV.PF.AQV
Retrocopy VMLPKPGTYSLHWEVSTSQVPGGVTLRTFGRLCLYDVI<QSGVTLMAQHGSDRHQVLVCTKLVKPFQAQV

Parental  GSLYVVLGELQHQQDRGSVVKARVLTCVEGMNLPLLEQAIREQRLYKQERGGSQ
          GSLY.VLG.LQ.QQ..GS.VKA.VL.CVEGM.LPL.EQA.REQR.Y...R.G.Q
Retrocopy GSLYLVLGGLQDQQ*GGSMVKALVLNCVEGMDLPL*EQAKREQRQY*RVRDGGQ

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	3.10 RPM
SRP007412_cerebellum	0.00 RPM	4.99 RPM
SRP007412_heart	0.00 RPM	1.57 RPM
SRP007412_kidney	0.00 RPM	7.06 RPM
SRP007412_liver	0.00 RPM	3.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3425 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3425 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3425 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2810
Macaca mulatta	retro_mmul_1164
Callithrix jacchus	retro_cjac_582

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013878	5 retrocopies	retro_cjac_3524, retro_cjac_3525, retro_cjac_3554, retro_cjac_3890, retro_cjac_582,
Gorilla gorilla	ENSGGOG00000013858	1 retrocopy	retro_ggor_2810,
Macaca mulatta	ENSMMUG00000029820	1 retrocopy	retro_mmul_1164,
Nomascus leucogenys	ENSNLEG00000001980	1 retrocopy	retro_nleu_1795,
Pongo abelii	ENSPPYG00000008646	1 retrocopy	retro_pabe_3425 ,