RetrogeneDB ID: retro_pabe_3629

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:37786138..37786461(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB1A
• Ensembl ID: ENSPPYG00000012284
• Aliases: MOB1A, MOBK1B, MOBKL1B
• Description: MOB kinase activator 1A [Source:UniProtKB/Swiss-Prot;Acc:Q5RAE0]

Sequence

>retro_pabe_3629
TCAGAACTCTACACTGAAGCAAGCTGTTCAGTCATGTCTTCAGGTCTAATATCTGAATATTATGGAGCAGGTGGTACTAA
TATTAATAATTCAGTCAAAGTTTTTGTTCCAAAATACATTGACTCTTTGATGGCCTAGCTTTAGGATTATATTGATCATG
AAACTTTTTTTCTTCTAATATTGGTGTCCCATTTTCCAAGAATTTTATATCTGTGGCCAAGACTATTAAGTGTCTGTTAA
AAGTTTATGCCCATATTTCTTACTAGCACTTTGGGTCTGTGGTGCAACCACAAGAAAACTCCCATGGCAACACCTTCTTC
AAG

Alignment

ORF - retro_pabe_3629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.18 %
• Parental protein coverage: 50.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TEFCTEASCPVMSAGPRYEYHWADGTNIKKPIKCSAPKYIDYLMTWVQDQLDDET-LFPSKIGVPFPKNF
          .E..TEASC.VMS.G...EY..A.GTNI....K...PKYID.LM....D..D.ET..F.S.IGVPF.KNF
Retrocopy SELYTEASCSVMSSGLISEYYGAGGTNINNSVKVFVPKYIDSLMA*L*DYIDHET<FFSSNIGVPFSKNF

Parental  MSVAKTILKRLFRVYAHIYHQHFDSVMQLQEEAHLNTSFK
          .SVAKTI.K.L..VYAHI...HF.SV.Q.QE..H.NT.FK
Retrocopy ISVAKTI-KCLLKVYAHISY*HFGSVVQPQENSHGNTFFK

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	12.50 RPM
SRP007412_cerebellum	0.00 RPM	22.86 RPM
SRP007412_heart	0.00 RPM	17.43 RPM
SRP007412_kidney	0.00 RPM	34.01 RPM
SRP007412_liver	0.00 RPM	20.26 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3629 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3629 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3629 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007277	1 retrocopy	retro_chof_502,
Echinops telfairi	ENSETEG00000018245	1 retrocopy	retro_etel_425,
Homo sapiens	ENSG00000114978	2 retrocopies	retro_hsap_1223, retro_hsap_4670,
Gorilla gorilla	ENSGGOG00000010015	1 retrocopy	retro_ggor_954,
Loxodonta africana	ENSLAFG00000014338	2 retrocopies	retro_lafr_223, retro_lafr_285,
Macaca mulatta	ENSMMUG00000015208	2 retrocopies	retro_mmul_1299, retro_mmul_297,
Nomascus leucogenys	ENSNLEG00000000321	2 retrocopies	retro_nleu_2161, retro_nleu_694,
Otolemur garnettii	ENSOGAG00000003504	1 retrocopy	retro_ogar_2688,
Pongo abelii	ENSPPYG00000012284	2 retrocopies	retro_pabe_1017, retro_pabe_3629 ,
Pan troglodytes	ENSPTRG00000012079	2 retrocopies	retro_ptro_3103, retro_ptro_837,
Rattus norvegicus	ENSRNOG00000042657	2 retrocopies	retro_rnor_2544, retro_rnor_2545,