RetrogeneDB ID: retro_pabe_2961

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:64955677..64956217(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM98
• Ensembl ID: ENSPPYG00000008166
• Aliases: None
• Description: transmembrane protein 98 [Source:HGNC Symbol;Acc:24529]

Sequence

>retro_pabe_2961
AAGGCCACGGTGATTGTTGCCATAAGCGTGCTGGCTACCATCTTTCTGGCTTTGTTTGCAGTCTTGGTGGTGGTTTGAGG
GCAGCGCTACCGCTGGCCAGGAGACCTGCTGCAGCGCTATGAATCCAAGCCCATTATGAGTCTCTTGGGTGCCATGGAGA
CCCAATCTGAGCTCTCTGAGTTAGAACTAGATGAGGTCATCATCGCCAACTCTGGCATAGAGCCCATTCTGGAGAATGAA
GACTGGATCTAGGATGCCTTGGGTCTCATGTCCCACTGCATTGTCATCTTGAAGATTTGTCACACTTTGAGAGAAAAACT
TGTTGCCATGACAACGGGTTCAGAGGCTGAGAAGACTTCAGCCACTGTCAGCAACATCATTGTGGTGGCCAAGTGGATCA
TCCCCAGAGTAGATGATGTTGTGAAATCAGTGTACCATCTGTTGAACACCAAGCTCCTGGATGTGAGTACCACTGCCCTG
CTCCTATCTGTCAGTTGTCAGGTGCTGGTAACCAGAAATGCCTGCCATCTGAACAGGGGC

Alignment

ORF - retro_pabe_2961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.59 %
• Parental protein coverage: 80.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETVVIVAIGVLATIFLASFAALVLVCRQRYCRPRDLLQRYDSKPIVDLIGAMETQSEPSELELDDVVITN
          ...VIVAI.VLATIFLA.FA.LV.V..QRY..P.DLLQRY.SKPI..L.GAMETQSE.SELELD.V.I.N
Retrocopy KATVIVAISVLATIFLALFAVLVVV*GQRYRWPGDLLQRYESKPIMSLLGAMETQSELSELELDEVIIAN

Parental  PHIEAILENEDWIEDASGLMSHCIAILKICHTLTEKLVAMTMGSGAKMKTSASVSDIIVVAKRISPRVDD
          ..IE.ILENEDWI.DA.GLMSHCI.ILKICHTL.EKLVAMT.GS.A..KTSA.VS.IIVVAK.I.PRVDD
Retrocopy SGIEPILENEDWI*DALGLMSHCIVILKICHTLREKLVAMTTGSEAE-KTSATVSNIIVVAKWIIPRVDD

Parental  VVKSMYPPLDPKLLDARTTALLLSVSHLVLVTRNACHLSGG
          VVKS.Y..L..KLLD..TTALLLSVS..VLVTRNACHL..G
Retrocopy VVKSVYHLLNTKLLDVSTTALLLSVSCQVLVTRNACHLNRG

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	1.66 RPM
SRP007412_cerebellum	0.00 RPM	12.52 RPM
SRP007412_heart	0.00 RPM	1.29 RPM
SRP007412_kidney	0.00 RPM	9.15 RPM
SRP007412_liver	0.00 RPM	4.59 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2961 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2961 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3605
Pan troglodytes	retro_ptro_2436
Pan troglodytes	retro_ptro_2990
Gorilla gorilla	retro_ggor_2432
Macaca mulatta	retro_mmul_1835
Callithrix jacchus	retro_cjac_2447

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014550	1 retrocopy	retro_cjac_2447,
Homo sapiens	ENSG00000006042	2 retrocopies	retro_hsap_1421, retro_hsap_3605,
Gorilla gorilla	ENSGGOG00000013333	2 retrocopies	retro_ggor_1098, retro_ggor_2432,
Myotis lucifugus	ENSMLUG00000001191	1 retrocopy	retro_mluc_130,
Macaca mulatta	ENSMMUG00000022356	2 retrocopies	retro_mmul_1835, retro_mmul_2256,
Nomascus leucogenys	ENSNLEG00000006038	3 retrocopies	retro_nleu_1233, retro_nleu_1840, retro_nleu_2635,
Pongo abelii	ENSPPYG00000008166	2 retrocopies	retro_pabe_1175, retro_pabe_2961 ,
Pan troglodytes	ENSPTRG00000008993	3 retrocopies	retro_ptro_2436, retro_ptro_2990, retro_ptro_971,