RetrogeneDB ID: retro_pabe_3759

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:53235995..53236817(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSPPYG00000007926
• Aliases: None
• Description: eukaryotic initiation factor 4A-I [Source:RefSeq peptide;Acc:NP_001126779]

Sequence

>retro_pabe_3759
TCCATGGATTATAACAGAGAACGTGGCAGCCCAGAGGGTATGGACCCCGATGGTGTCATTGAGAGGAACTGGAATGAGAT
TGTTGATAACTTTGATGATATGAATTTAAAGGAGTCTCTTCTTTGGGGCATCTATGCTTACGATTTTGAGAAGTCTTCTG
CTATTCAGCAGAGAGCTATTATTACCTGTATGAAAGGGTATGATGTGATTGCTCAAGCTCAGTCAGGTACTGGCAAGACA
GCCACATTTGCTATTTCCATCTTGCAACAGTTGGAGACCCAAGCACTAATGCTGGCCCTCACCAGAGAACTAGCTCCACA
GATCCAAAAGGTAATTCTGGCACTTGGAGACTATATGGGAGCAACTTGTCATGTCTGCATTGGTGGAACAAATGTTCGAA
CTGAAATGCAAAAACTGCAGGCTGAAGCACCACATATTGTTGTTGGTACACCTGGGAGAGTGTTTGATATGTTAAACAGA
AGATATCTTTTTCCAAAATGGATCAAAATGCTTGTTTGGGATGAAGCAGATGAAATGTTGAGCCGTGGGTTTAAAGATGA
AATCTATGAGATTTTCCAAAAACTAAATACAAGTATTCAGGTTGTGTTGCTTTCTGCCACAATGCCAACTGATGTATTGG
AAGTGACCAAAAAATTCATGAGAGATCCAATTCGAATTCTGGTGAAAAAGGAATAATTGACCCTTGAAGGAATCAAAAAG
TTTTATATTAATGTTGAGAGAGAGGAGTGGAAGTTGGATACACTTTGTGGCTTGTACGAGACACTGACCATTACGCAGGC
TGTTATTTTTCTCAAGGCCCAA

Alignment

ORF - retro_pabe_3759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.91 %
• Parental protein coverage: 68.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVI
          S.D.......P.GM.P.GVIE.NWNEIVD.FDDMNL.ESLL.GIYAY.FEK.SAIQQRAI..C.KGYDVI
Retrocopy SMDYNRERGSPEGMDPDGVIERNWNEIVDNFDDMNLKESLLWGIYAYDFEKSSAIQQRAIITCMKGYDVI

Parental  AQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAE
          A..Q...G...T....I.....L....TQAL.LA.TRELA.QIQKV..ALGDYMGA.CH.CIGGTNVR.E
Retrocopy A--QAQSGTGKTATFAISILQQLE---TQALMLALTRELAPQIQKVILALGDYMGATCHVCIGGTNVRTE

Parental  VQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLS
          .QKLQ.EAPHI.VGTPGRVFDMLNRRYL.PK.IKM.V.DEADEMLSRGFKD.IY.IFQKLN...QVVLLS
Retrocopy MQKLQAEAPHIVVGTPGRVFDMLNRRYLFPKWIKMLVWDEADEMLSRGFKDEIYEIFQKLNTSIQVVLLS

Parental  ATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTR
          ATMP.DVLEVTKKFMRDPIRILVKKE.LTLEGI..FYINVEREEWKLDTLC.LYETLTITQAVIF....
Retrocopy ATMPTDVLEVTKKFMRDPIRILVKKE*LTLEGIKKFYINVEREEWKLDTLCGLYETLTITQAVIFLKAQ

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	0.17 RPM	64.30 RPM
SRP007412_cerebellum	0.00 RPM	43.53 RPM
SRP007412_heart	0.06 RPM	66.17 RPM
SRP007412_kidney	0.03 RPM	95.73 RPM
SRP007412_liver	0.03 RPM	142.08 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3759 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3759 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3759 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000132	1 retrocopy	retro_btau_1207,
Loxodonta africana	ENSLAFG00000001107	1 retrocopy	retro_lafr_1210,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Oryctolagus cuniculus	ENSOCUG00000010375	5 retrocopies	retro_ocun_1020, retro_ocun_1326, retro_ocun_1375, retro_ocun_475, retro_ocun_934,
Pongo abelii	ENSPPYG00000007926	7 retrocopies	retro_pabe_1090, retro_pabe_1474, retro_pabe_3759 , retro_pabe_3792, retro_pabe_548, retro_pabe_846, retro_pabe_987,
Pongo abelii	ENSPPYG00000014384	2 retrocopies	retro_pabe_596, retro_pabe_677,