RetrogeneDB ID: retro_ptro_423

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:44711674..44713202(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2A
• Ensembl ID: ENSPTRG00000015528
• Aliases: None
• Description: None

Sequence

>retro_ptro_423
GGATCAGAAGGACTCTGTATGGTGAATGCACCACCATGTTTTGCAGAAAGCATAGTGTTTCCAAGGAAATCTCAGGAAAA
TTACAAAATCTGTAACTTTAGCAACAGTTGGAGCTTCATTTGCTGGGGCAAAGGAAAAAAATTATAAATATTATCAGTGT
CACTAACATGAGTTTACTACACTTCTTCCACCTGCAAAGGCACTTTTTTCTTGAATTCTTACCAAAAACCCATGTCCTGG
TAATACAGCAGCCTTACACTTCCCTACACATGGCACTCCTGGGAGACTCAACCTGCAACTCCATCGTGTGAGAGTGGGAT
GTGCCTGAAGTCTTTCATCAAGGAAAAAATGTAAATTGGTATCCATCTGGTCAGATGATGAAACTGTTTTGTGTCCAAAA
TGTTAACAATAAAGTTCACTTCTTTGTAAATGATGATTTTATAAAATTGCAAGTAAATTGTCTTTGCAGAAAATTAATTG
TGGGTTATCACTTGGACTCCAATCACACAAGGGGGCTGTCTATGTTTCAGGGAGTAAGGGTGTACTTTCATTTGTTGTAT
TATACTCGTACCCCAACTTTTTTGGACCTCATGCAGCTTTAGCCAACAGCAGTTTCTCTAAGCCGATGAGGTTACAACGC
TGTGGAATGAAAAATCCACTGCTGGCTTGTAATAGCGAGAACAGATGTTGACAAGAGAAGAACTTCCTGCTATGGGGAAC
AAAGGCTGCATTGCACTGCAACAAATGGAGAAAGTGCTGTCATTTGTTCAATTACCAAAACATAGCCCCATTTATGATAT
AATTTGGAATTCTGGTTCTACTGAGTTTTATGCTATTTATGGTTTTATGCCTGCCAAAGCTATGATTTTCAACTTGAAAT
GTGATCTTGTGTTTGACCTTGGAACTGGTGCTCTAGCGCAGCCTATTCGGCCCTTGTGGCCATATATTAATACTAACTAG
ATTTGGAAATCTGAGGAACAAACGTGAGTGTGGGATATTAAAAGCTACAAACTTATTTCCAAACAAGTATCCTCTGATCA
TACATATTTTGCTAGGTACCTAGATGGGAGCACCTTTTACTATCACACATGCTCCCAGGTTGTGTGTTAATAATGGATAC
AAGCTTTGACATTATACCAGCCCTATCCTGCATGAGTAAGATGTGTCACCAAATGTAGAAATATGGCAGGCTTCTTGGCA
GCCATTTCTGGATGAACTATTTCCAGCAAAAGCAGTAACTTATCAAGCAGTTCCAAGTGAAGTACCCAACTAGGAACCTA
AATTTGCAACGACTGATAGACTCCCAGCTTTAAGAAATAAAACAATCACCAATTCTAAGCTGTATGAAGAGAAATCACCC
CAGAATAAGAAATCCCAACCAGGAAATGATAAACCATTAACAAAAGCAGCCCTGAAAAATCAAAGGAAATATAAAGCTAA
GAAAGCTACAAAGCAGGAAGTAAGAAGTGACAAGAGTCCAGATTTGACACCTACCCCTGTCCCCCAGAGCACACCCTGAA
ATACAGTG

Alignment

ORF - retro_ptro_423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.65 %
• Parental protein coverage: 87.52 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 15

Retrocopy - Parental Gene Alignment:

Parental  GSEGLYMVNGPPHFTESTVFPRESGKNCKVYTFSKDGTLFAW-GNGEKV-NIISVTNKGLLHSFDLPKAV
          GSEGL.MVN.PP.F.ES.VFPR.S..N.K...FS.......W.G...K..NIISVTN..LLH.F.L....
Retrocopy GSEGLCMVNAPPCFAESIVFPRKSQENYKICNFSNSWSFICW<GQRKKIINIISVTNMSLLHFFHLQRHF

Parental  CLEFSPKNTVLATWQPYTT-SKDGTAGIPNLQLYDVK-TGTCLKSFIQKKM-QNWCPS-WSEDETL-CAR
          .LEF.PK..VL...QPYT.....GT.G..NLQL..V...G.CLKSFI..KM..NW.PS.WS.DET..C..
Retrocopy FLEFLPKTHVLVIQQPYTS<PTHGTPGRLNLQLHRVR<SGMCLKSFIKEKM<VNWYPS<WSDDETV>CVQ

Parental  SVNNEVHFFENNNF-NTIANKLHLQKINDFVLSPGPQPYKVAVYVPGSKGAPSFVRLYQYPNFAGPHAAL
          .VNN.VHFF.N..F...IA.KL.LQKIN...LS.G.Q..K.AVYV.GSKG..SFV.LY.YPNF.GPHAAL
Retrocopy NVNNKVHFFVNDDF<YKIASKLSLQKIN-CGLSLGLQSHKGAVYVSGSKGVLSFVVLYSYPNFFGPHAAL

Parental  ANKSFFK-ADKVTMLWNKKATA-VLVIASTDVDKTGASYYGEQTLHYIATNGESAVV-QLPKNGP-IYDV
          AN.SF.K.AD.VT.LWN.K.TA..LVIA.TDVDK...S.YGEQ.LH..ATNGESAV.....K..P.IYD.
Retrocopy ANSSFSK<ADEVTTLWNEKSTA<WLVIARTDVDKRRTSCYGEQRLHCTATNGESAVICSITKT*P>IYDI

Parental  VWNSSSTEFCAVYGFMPAKATIFNLKCDPVFDFGTGP-RNAAY-YSPHGHILVLAGFGNLRGQME-VWDV
          .WNS.STEF.A.YGFMPAKA.IFNLKCD.VFD.GTG....AAY...P.GHIL.L..FGNLR...E.VWD.
Retrocopy IWNSGSTEFYAIYGFMPAKAMIFNLKCDLVFDLGTGA<SSAAY<FGPCGHILILTRFGNLRNKRE<VWDI

Parental  KNYKLISKPVASDSTYFAWCPDG-EHIL-TATCAPRLRVNNGYKIWHYTGSILHKYDVPSNAELWQVSWQ
          K.YKLISK.V.SD.TYFA...DG.EH.L.T.T.APRL.VNNGYK..HYT..ILH..DV..N.E.WQ.SWQ
Retrocopy KSYKLISKQVSSDHTYFARYLDG<EHLL<TITHAPRLCVNNGYKL*HYTSPILHE*DVSPNVEIWQASWQ

Parental  PFLDGIFPAKTITYQAVPSEVPNEEPKVATAYRPPALRNKPITNSKLHEEEPPQNMKPQSGNDKPLSKTA
          PFLD..FPAK..TYQAVPSEVPN.EPK.AT..R.PALRNK.ITNSKL.EE..PQN.K.Q.GNDKPL.K.A
Retrocopy PFLDELFPAKAVTYQAVPSEVPN*EPKFATTDRLPALRNKTITNSKLYEEKSPQNKKSQPGNDKPLTKAA

Parental  LKNQRKHEAKKAAKQEARSDKSPDLAPTPAPQSTPRNTV
          LKNQRK..AKKA.KQE.RSDKSPDL.PTP.PQSTP.NTV
Retrocopy LKNQRKYKAKKATKQEVRSDKSPDLTPTPVPQSTP*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	24.65 RPM
SRP007412_cerebellum	0.00 RPM	67.47 RPM
SRP007412_heart	0.00 RPM	42.67 RPM
SRP007412_kidney	0.00 RPM	48.35 RPM
SRP007412_liver	0.00 RPM	37.19 RPM
SRP007412_testis	0.32 RPM	19.92 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_423 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_423 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_423 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_565
Gorilla gorilla	retro_ggor_509
Pongo abelii	retro_pabe_517
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,