RetrogeneDB ID: retro_pabe_517

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:43392379..43393142(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2A
• Ensembl ID: ENSPPYG00000029636
• Aliases: None
• Description: eukaryotic translation initiation factor 2A, 65kDa [Source:HGNC Symbol;Acc:3254]

Sequence

>retro_pabe_517
GTTCAATTACCAAAACTTAGCCCCATTTGTGATATAATTTGGAATTCTGGTTCTACTGAGTTTTATGCTATTTATGGTTT
TATGCCTGCCAAAGCTATGATTTTCAACTTGAAATGTGATCTTGTGTTTGACCGTGGAACTAGTGCTCTAAGGCAGCCTA
TTTGGCCCTTGTGGCCATATATTAATACTAACTGGATTTGGAAATCTGAGGAACAAACATGAGTGTGGGATATTAAAAGC
TACAAACTTATTTCCAAACAAGTAGCCTCTGATCATACATATTTTGCTAGGTACCTAGATGGGAGCACCTTTTACTATCA
CACATGCTCCCAAGTTGTGTGTTAATAATGGATACAAGCTTTGACATTACACCAGCCCTATCCTGCATGAGTAAGATGTG
TCACCAAATGTAGAAATACGGCAGGTTTCTTGGCAGCCATTTCTGGATGAACTATTTCCAGCAAAAGCAGTAACCTATCA
AGCAGTTCCAAGTGAAGTACCCAACTAAGAACCTAAATTTGCAATGACTGATAGACTCCCAGCTTTAAGAAATAAACCAA
TCACCAATTCCAAGCTGCATGAAGAGAAATCACCCCAGAATAAGAAATCACAACCAGGAAATGATAAACCATTAACAAAA
GCAGCCCTCAAAAATCAAAGGAAATATGAAGCTAAGAAAGCTACAAAGCAGGAAGTAAGAAGTGACAAGAGTCCAGATTT
GACACCAACCCCTGTCCCGCAGAGCACACCCTGAAATACAGTG

Alignment

ORF - retro_pabe_517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.65 %
• Parental protein coverage: 71.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VQLPKNGPIYDVVWNSSSTEFCAVYGFMPAKATIFNLKCDPVFDFGTGP-RNAAY-YSPHGHILVLAGFG
          VQLPK..PI.D..WNS.STEF.A.YGFMPAKA.IFNLKCD.VFD.GT.....AAY...P.GHIL.L.GFG
Retrocopy VQLPKLSPICDIIWNSGSTEFYAIYGFMPAKAMIFNLKCDLVFDRGTSA<SKAAY<FGPCGHILILTGFG

Parental  NLRGQME-VWDVKNYKLISKPVASDSTYFAWCPDG-EHIL-TATCAPRLRVNNGYKIWHYTGSILHKYDV
          NLR...E.VWD.K.YKLISK.VASD.TYFA...DG.EH.L.T.T.AP.L.VNNGYK..HYT..ILH..DV
Retrocopy NLRNKHE<VWDIKSYKLISKQVASDHTYFARYLDG<EHLL<TITHAPKLCVNNGYKL*HYTSPILHE*DV

Parental  PSNAELWQVSWQPFLDGIFPAKTITYQAVPSEVPNEEPKVATAYRPPALRNKPITNSKLHEEEPPQNMKP
          ..N.E..QVSWQPFLD..FPAK..TYQAVPSEVPN.EPK.A...R.PALRNKPITNSKLHEE..PQN.K.
Retrocopy SPNVEIRQVSWQPFLDELFPAKAVTYQAVPSEVPN*EPKFAMTDRLPALRNKPITNSKLHEEKSPQNKKS

Parental  QSGNDKPLSKTALKNQRKHEAKKAAKQEARSDKSPDLAPTPAPQSTPRNTV
          Q.GNDKPL.K.ALKNQRK.EAKKA.KQE.RSDKSPDL.PTP.PQSTP.NTV
Retrocopy QPGNDKPLTKAALKNQRKYEAKKATKQEVRSDKSPDLTPTPVPQSTP*NTV

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	14.65 RPM
SRP007412_cerebellum	0.00 RPM	33.32 RPM
SRP007412_heart	0.00 RPM	14.15 RPM
SRP007412_kidney	0.00 RPM	24.76 RPM
SRP007412_liver	0.00 RPM	23.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_517 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_517 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_565
Pan troglodytes	retro_ptro_423
Gorilla gorilla	retro_ggor_509
Macaca mulatta	retro_mmul_2395

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001199	1 retrocopy	retro_cjac_968,
Dasypus novemcinctus	ENSDNOG00000014002	1 retrocopy	retro_dnov_1148,
Homo sapiens	ENSG00000144895	1 retrocopy	retro_hsap_565,
Gorilla gorilla	ENSGGOG00000015391	1 retrocopy	retro_ggor_509,
Loxodonta africana	ENSLAFG00000003767	1 retrocopy	retro_lafr_502,
Macaca mulatta	ENSMMUG00000017696	1 retrocopy	retro_mmul_2395,
Nomascus leucogenys	ENSNLEG00000003219	1 retrocopy	retro_nleu_2213,
Oryctolagus cuniculus	ENSOCUG00000016095	3 retrocopies	retro_ocun_1771, retro_ocun_1825, retro_ocun_1861,
Pongo abelii	ENSPPYG00000029636	2 retrocopies	retro_pabe_517 , retro_pabe_652,
Pan troglodytes	ENSPTRG00000015528	1 retrocopy	retro_ptro_423,
Ictidomys tridecemlineatus	ENSSTOG00000003374	1 retrocopy	retro_itri_1706,