RetrogeneDB ID: retro_pabe_3429

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:82980761..82981418(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3J
• Ensembl ID: ENSPPYG00000006431
• Aliases: None
• Description: eukaryotic translation initiation factor 3 subunit J [Source:RefSeq peptide;Acc:NP_001126147]

Sequence

>retro_pabe_3429
GGGGACCGCTGCAAAGGCAAGGAATAGGACAAGGATGAGGACGTCTAGGATAACTGGGATGATGGTGATGACAGGAAAAA
GAAAAAAGAGGAAGCAGAAGTAAACATTTTAGAAAAGAAAAAATTAACAGAGAAGATAAAACAGAAAGAACGGCAACAGA
AGAAAGGGCAGGAAGAAATTAAAAAGGGGTTACAAGAACCTGAAGAACTCCAGGTGCTAACACTAGAGGAACAATTAGCA
GATAAACCGCAGCTGGAGAAATCACAGGATGAGTCAGACATGGAATTAGCAAAGGCAACTTCTGGTGTTAAGACTACTGT
ATATGGAACGGATGCTATAAACCCATCTTCAAGGGATGACCTTACAGAGTTTGGAAAGTTACTAAAAGATAAAATTACAC
AAAATAAAAAGTCACTATATTATGCCAGTTTTTTGGAAGTCTTAGTTGGAGATGTGTGTATGTCATTGGAAACTGATGAC
TTGAAAAAGGTTCTCAATACATTGTGCTTTGAAGTGAAAAACAGAAGTAAGCAAAGCCAAGCCAAAAAGAACAAAGGTAT
GGTTCCTGGAGGGAGATTAAAAGCCACCATGACAAATGATCTGGTAAATTATGGTGGTGATGATGCAGGGTATGCACAAG
ACTATGAAAACGTCATG

Alignment

ORF - retro_pabe_3429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.27 %
• Parental protein coverage: 86.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDRWEGE--DEDEDVKDNWDDDDDEKKEEAEVKPEVKISEKKKIAEKIKEKERQQKKRQEEIKKRLEEPE
          GDR..G...D.DEDV.DNW..DD......................EKIK.KERQQKK.QEEIKK.L.EPE
Retrocopy GDRCKGKE*DKDEDV*DNW--DDGDDXXXXXXXXXXXXXXXXXLTEKIKQKERQQKKGQEEIKKGLQEPE

Parental  EPKVLTPEEQLADKLRLKKLQEESDLELAKETFGVNNTVYGIDAMNPSSRDDFTEFGKLLKDKITQYEKS
          E..VLT.EEQLADK..L.K.Q.ESD.ELAK.T.GV..TVYG.DA.NPSSRDD.TEFGKLLKDKITQ..KS
Retrocopy ELQVLTLEEQLADKPQLEKSQDESDMELAKATSGVKTTVYGTDAINPSSRDDLTEFGKLLKDKITQNKKS

Parental  LYYASFLEVLVRDVCISCNVSGTKGFCVFMRVAVPDKMAHKQSKAKKKKKGVVPGGGLKATMKDDLADYG
          LYYASFLEVLV.DVC.S......K...V........K...KQS.AKK.K.G.VPGG.LKATM..DL..YG
Retrocopy LYYASFLEVLVGDVCMSLETDDLKK--VLNTLCFEVKNRSKQSQAKKNK-GMVPGGRLKATMTNDLVNYG

Parental  GYDGGYVQDYEDFM
          G.D.GY.QDYE..M
Retrocopy GDDAGYAQDYENVM

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	11.78 RPM
SRP007412_cerebellum	0.00 RPM	5.96 RPM
SRP007412_heart	0.00 RPM	11.71 RPM
SRP007412_kidney	0.00 RPM	11.70 RPM
SRP007412_liver	0.00 RPM	8.14 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3429 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3429 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4189
Gorilla gorilla	retro_ggor_41

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Dipodomys ordii	ENSDORG00000008339	7 retrocopies	retro_dord_208, retro_dord_364, retro_dord_451, retro_dord_470, retro_dord_633, retro_dord_738, retro_dord_746,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Pongo abelii	ENSPPYG00000006431	1 retrocopy	retro_pabe_3429 ,