RetrogeneDB ID: retro_pabe_548

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:90855819..90856658(+)
• Located in intron of: ENSPPYG00000002481

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_548
TCCAGAGACAATGGTCCTGATGAGATGGAGCCTGAAGGCATCATTGAGAGAAACTGAAATGAGATTGTTGACAGTTTTGA
TGATATGAACCTCTTGGAATCCCTCCTCCATGGCATCTATGCCTATGGTTTTGAGAAGTCCTCTGCCATCCAGCAGCGAG
CCATTCTTCTTGTATCAAGGGTTATGATGTGATCACTCAAGCCCTATCTGGGACTGGGAAAATGGCCACTTTTGCCATAT
CAATTCTGCAGGAGATTGAATTAGATCTAAAGGCTACCACGCCTTGGTCCTAGCATCCACTTGATAATTGGCTCAAAAGA
TAGAAAAGGTGGTCATGACACTAGGAGACTACATGGGTGCCTCCTGTCATGCCTGTATTGGGGGCACCAACGTGCATGCT
GAGGTGCAGAAACTGCAGATGGAAGTTCCCGGTATCATCGTGGGTACCCCTGGCCATAAGTTTGATATGCTTAACCAGAG
ATACCTGTCTCCCAAATACATCAAGATGTTTGTACTGGACGAAGCTGATGAAATGTTAAGCCATGGATTCAAGGACTCAA
TCTATGACATATTCCAAAAGCTCAACAGCAACACCCAGATGATTTTGCTATCAGCCACAAGGCCTTCTGACGTGCTTGAG
GTGACCAAGAAGTTCATGAGGGACCCCATTTGGATTCCTGTCAAGAAGGAAGAGTTGACCCTGGAGGGGATCCACCAATT
CTACATCAATGTGGAACATGAGGAGTGGAAGCTGAGCACACTGCGTGACTTGTATGAAACCCTGACTGTCACCCTAGGCA
GTCATCTTCATCAATACTGGAAAGAAGGTGGATTGGCTC

Alignment

ORF - retro_pabe_548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.81 %
• Parental protein coverage: 68.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAIL-PCIKGYDVIAQAQ
          SRDNGPD.MEPEG.IE.N.NEIVDSFDDMNL.ESLL.GIYAYGFEK.SAIQQRAIL..CIKGYDVI.QA.
Retrocopy SRDNGPDEMEPEGIIERN*NEIVDSFDDMNLLESLLHGIYAYGFEKSSAIQQRAIL<SCIKGYDVITQAL

Parental  SGTGKTATFAISILQQIELDLKAT-QALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQK
          SGTGK.ATFAISILQ.IELDLKAT..ALVLA.T..LAQ.I.KVVM.LGDYMGASCHACIGGTNV.AEVQK
Retrocopy SGTGKMATFAISILQEIELDLKAT<HALVLAST**LAQKIEKVVMTLGDYMGASCHACIGGTNVHAEVQK

Parental  LQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATM
          LQME.P.IIVGTPG..FDMLN.RYLSPKYIKMFVLDEADEMLS.GFKD.IYDIFQKLNSNTQ..LLSAT.
Retrocopy LQMEVPGIIVGTPGHKFDMLNQRYLSPKYIKMFVLDEADEMLSHGFKDSIYDIFQKLNSNTQMILLSATR

Parental  PSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQ-AVIFINTRRKV
          PSDVLEVTKKFMRDPI.I.VKKEELTLEGI.QFYINVE.EEWKL.TL.DLYETLT.T..AVIFINT..KV
Retrocopy PSDVLEVTKKFMRDPIWIPVKKEELTLEGIHQFYINVEHEEWKLSTLRDLYETLTVTL>AVIFINTGKKV

Parental  DWL
          DWL
Retrocopy DWL

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	0.06 RPM	64.30 RPM
SRP007412_cerebellum	0.12 RPM	43.53 RPM
SRP007412_heart	0.06 RPM	66.17 RPM
SRP007412_kidney	0.20 RPM	95.73 RPM
SRP007412_liver	0.00 RPM	142.08 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_548 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_548 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_548 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_610
Pan troglodytes	retro_ptro_450
Gorilla gorilla	retro_ggor_537

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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,