RetrogeneDB ID: retro_pabe_2283

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:10035185..10036301(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSPPYG00000025848
• Aliases: None
• Description: eukaryotic translation initiation factor 4B [Source:HGNC Symbol;Acc:3285]

Sequence

>retro_pabe_2283
CGGGAGGGGTATCAGGATGGCCCACGCTGGGATCGATATGGCGGCCAGGATCGCTATGATGACCCAGGCAGCAGACACTA
TGATAGAGGCTATGATTCCCAGATAGGCAATGGCAGAAGAGCATTTGATAGTGGGTACCGCAGGGATAATGACTACAGAG
AAGGCAGGGACCGCTCTGAAGACCGATACAACAGACGGGATGATCGGTCGTGGAGCTCCAGAGATGATTACACTTGGGAT
GATTATAGGTGTGATGATAGAGGTCCCCCGCAAAGACCCAAACTGAATCTAAAGCTTTGGAGTACTCCTAAGGAAGATGA
TTCCTCTGCTAGTACCTCTCAGTCCAGTCGAGCTGCTTCTGTCTTTCTTTGGAGGGGCAAAGCCCGTTGACACAGCCGCT
AGAGAAAGAGAAGTAGAAGAAATGCTACAGAACAAGAGAAGTTGCAGCGTCAGCTGGATGAGCCATAACTAGAACGACGG
CCTCGGGAGAGACACCCAAGCTGGCAAAGTGAAGAAACTCAAGAATGGAGTGGTCGCGGACAGGAAGTGAGTCATGGCAG
ACTGAGACCTCCGCCACATCCGGCAGAAATGCACGAAGGAGAGAGAGTGAGAAGTCTCTAGAAAATGAAACACTCAATAA
GGAGGAAGATTGTCACTCTCCAACTTCTAAACGTCCCAAACCTGATCCTGCCAGACCCAAAGATAATGCCAGCCCCTCCA
CCAAAGGAGAATGCTTCGGTGAAGCGAAGTTCTAACCCTCCTGCTCCATCTCAGAGCTCAGACACAGAGCAGCAATCCCC
TACAAGTGGTGGGGGAAAAGTTACTCCAGCTCAATCATCTGAGGAAGGACCAGCAAAGAAAGATGAAAATAAAGTGGATG
GGATGAAAGTCCCAAAAGGTCAAACTGGGAACTCTAGCTGTGGTCCAGGAGATGGAGGGAGCAAAGACCACTGAAAGGAG
TCAGATAGGAAAGATGGCAAAAAGGATCAAGACTCCAGATCTGCACCTGAGCCAAAGAAACCTGAGGAAAATCTAGCTTC
CAAGTTGAGTTCTGCAAGCAAGTATGCTGCTGTCTCCCTTTCTGGTGAAGATGAAAACAAGGGAGAAGATTACGCC

Alignment

ORF - retro_pabe_2283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.05 %
• Parental protein coverage: 61.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGSGYRRDDDYRGGGDRYEDRYDRRDD
          R.GY.DGPR...DRYGG.DRYDD.GSR.YDRGYDS.IG.GRRAF.SGYRRD.DYR.G.DR.EDRY.RRDD
Retrocopy REGYQDGPR--WDRYGGQDRYDDPGSRHYDRGYDSQIGNGRRAFDSGYRRDNDYREGRDRSEDRYNRRDD

Parental  RSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQSTRAASIFGGAKPVDTAAREREVE
          RSWSSRDDY..DDYR.DDRGPPQRPKLNLK..STPKEDDSSASTSQS.RAAS.F..........R.R...
Retrocopy RSWSSRDDYTWDDYRCDDRGPPQRPKLNLKLWSTPKEDDSSASTSQSSRAASVFLWRGKAR*HSR*RKRS

Parental  ERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQE-RERSRTGSESSQTGTSTTSGRNARRRESEKSL
          .R...EQEKLQRQLDEP.LERRPRERHPSW.SEETQE..E.SRTGSES.QT.TS.TSGRNARRRESEKSL
Retrocopy RRNATEQEKLQRQLDEP*LERRPRERHPSWQSEETQE<MEWSRTGSESWQTETSATSGRNARRRESEKSL

Parental  ENETLNKEEDCHSPTSKPPKPDQ-PLKVMPAPPP-KENAWVKRSSNPPARSQSSDTEQQSPTSGGGKVAP
          ENETLNKEEDCHSPTSK.PKPD..P.......PP.KENA.VKRSSNPPA.SQSSDTEQQSPTSGGGKV.P
Retrocopy ENETLNKEEDCHSPTSKRPKPDP>PDPKIMPAPPPKENASVKRSSNPPAPSQSSDTEQQSPTSGGGKVTP

Parental  AQPSEEGPARKDENKVDGMNVPKGQTGNSSRGPGDGGNKDHWKESDRKDGKKDQDSRSAPEPKKPEENPA
          AQ.SEEGPA.KDENKVDGM.VPKGQTGNSS.GPGDGG.KDH.KESDRKDGKKDQDSRSAPEPKKPEEN.A
Retrocopy AQSSEEGPAKKDENKVDGMKVPKGQTGNSSCGPGDGGSKDH*KESDRKDGKKDQDSRSAPEPKKPEENLA

Parental  SKFSSASKYAALSVDGEDENEGEDYA
          SK.SSASKYAA.S..GEDEN.GEDYA
Retrocopy SKLSSASKYAAVSLSGEDENKGEDYA

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	52.30 RPM
SRP007412_cerebellum	0.00 RPM	30.52 RPM
SRP007412_heart	0.03 RPM	59.18 RPM
SRP007412_kidney	0.00 RPM	74.45 RPM
SRP007412_liver	0.00 RPM	56.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2283 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2283 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1882
Macaca mulatta	retro_mmul_1428

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000017489	2 retrocopies	retro_pabe_1879, retro_pabe_1988,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283 , retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,