RetrogeneDB ID: retro_nleu_2213

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397335.1:2786801..2788316(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2A
• Ensembl ID: ENSNLEG00000003219
• Aliases: None
• Description: None

Sequence

>retro_nleu_2213
CTACACTTCTTCCACCTCCAAAGGCACTTTGCCTTGAATTCTTACCAAAAACCCATGTCCTGGTAATACAGCAGCCTTAC
GCTTCCCTACACATGGCACTCCTGGGAGACTCAACCTGCAACTCCATTGTGTGAGAGTGGGGTGTGCTTGAAGTCTTTCA
TCAAGAAAAAAATGCAGATTGGTATCCATCTGGTCACATGAAACTGTTTTGTGTCCAAAATGTTAACAATAAAGTTCACT
TCTTTGTAAACAACGATTTTATAAAATTGCAAGTAAGTTGTCTTTGCAAAAAATTAATTGTGGATTATCACTTGGACTCC
AGTCACAAAAGGTGACTGTCTATGTTCCAGGGAGTAAGGGTGTACTTTCATTTGTTGTATTATACTCGTACCCCAACTTT
TTTGGACCTCATGCAGCTTTAGCCAACAGCAGTTTCTCTAAGCCGATGAGGTTACAACACTGTGGAATGAAAAAGCCACT
GCTGGCTTGTAATAGTGAGAACAGATGTTGACAAGACAAGAACTTCCTGCTATGGGGAACAAAGGCTGCATTGCACTGCA
ACAAATGGAGAAAGTGCTGTCATTTGTTCAATTACCAAAACGTAGCCCCATTTATGATATAATTTGGAATTCTGGTTCTA
CTGAGTTTTATGCTATTTATGGTTTTATGCCTGCCAAAGCTATGATTTTCAACTTGAAATGTGATCTTGCATTTGACCTT
GGAACTGGTGCTCTGAGGCAGCCTATTTGGCCCTTATGGCCATATGTTAATACTAACTGGATTTGGAAATCTGAGGAACA
AACATGAGTGTGGGATATTAAAAGCTACAAACTTATTTCCAAACAAGTAGCCTCTGATCATACATATTTTGCTAGGTACC
TAGATGGGAGCACCTTTTACTATCACACATGCTCCCAGGTTGTGTGTTAATAATGGATACAAGTTTGACATTATACCAGC
TCTATCCTGCATGAGTAAGATGTGTCACCAAATGTAGAAATACGGCAGGTTTCTTGGCAGCCATTTCTGGATGAACTATT
TCCAGCAAAAGCAGTAACTTATCAAGCAGTTCCAAGTGAAATACCCAACTAGGAACCTAAATTTGCAATGACTGGTAGAC
TCCCAGCTTTAAGAAATAAACTAATCACCAATTCTAAGCTGCATGAAGAGAAATCACCCCAGAATAAGAAATCACAACCA
GGAAATGATAAACCATTATCAAAAGCAGCCTTGAAAAATCAAAGGAAATATAAAGCCAAGAAAGCTACAAAGCAGGAAGT
AAGAAGTGACAAGAGTCCAGATTTGACACCTACCCCTGTCCCACAGAGCACACCCTGAAATACAGTCTCAGTTAACATCT
GGAAACCCTGAGATAGACGAAAAATTCAAGAAACTAAAAAGTCAAAAGCAGCTGAACCTTGAAAGAACACAGTAACTGAA
ACACAGCTAGAAAAACAATGAGTTAGAAAAATAAAAGATACTTCCCTTCTTCAAGAGCTGGAAGATTTGAAAATG

Alignment

ORF - retro_nleu_2213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.89 %
• Parental protein coverage: 87.71 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 14

Retrocopy - Parental Gene Alignment:

Parental  LHSFDL-PKAVCLEFSPKNTVLVTWQPYTT-SKDGTAGIPNLQLYDVK-TGMHLKSFIQKKLQ-NWCPSW
          LH.F.L.PKA.CLEF.PK..VLV..QPY......GT.G..NLQL..V...G..LKSFI.KK.Q..W.PS.
Retrocopy LHFFHL<PKALCLEFLPKTHVLVIQQPYAS<PTHGTPGRLNLQLHCVR<SGVCLKSFIKKKMQ<DWYPS-

Parental  SEDETLCARNVNNEVHFFENNNF-NTIVSKLHLQKINDFVLSPGPQPYKVAVYVPGSKGAPSFVRLYQYP
          ......C..NVNN.VHFF.NN.F...I.SKL.LQKIN...LS.G.Q..KV.VYVPGSKG..SFV.LY.YP
Retrocopy GHMKLFCVQNVNNKVHFFVNNDF<YKIASKLSLQKIN-CGLSLGLQSQKVTVYVPGSKGVLSFVVLYSYP

Parental  NFAGPHAALANKSFFK-ADKVTMLWNKKATA-VLVIASTDVDKTGASYYGEQTLHYIATNGESAVV-QLP
          NF.GPHAALAN.SF.K.AD.VT.LWN.KATA..LVI..TDVDKT..S.YGEQ.LH..ATNGESAV.....
Retrocopy NFFGPHAALANSSFSK<ADEVTTLWNEKATA<WLVIVRTDVDKTRTSCYGEQRLHCTATNGESAVICSIT

Parental  KNGP-IYDVVWNSSSTEFCAVYGFMPAKATIFNLKCDPVFDFGTGP-RNAAY-YSPHGHILVLAGFGNLR
          K..P.IYD..WNS.STEF.A.YGFMPAKA.IFNLKCD..FD.GTG....AAY...P.GH.L.L.GFGNLR
Retrocopy KT*P>IYDIIWNSGSTEFYAIYGFMPAKAMIFNLKCDLAFDLGTGA<SEAAY<FGPYGHMLILTGFGNLR

Parental  GQME-VWDVKNYKLISKPVASDSTYFAWCPDG-EHIL-TATCAPRLRVNNGYK-IWHYTGSVLHKYDVPS
          ...E.VWD.K.YKLISK.VASD.TYFA...DG.EH.L.T.T.APRL.VNNGYK...HYT.S.LH..DV..
Retrocopy NKHE<VWDIKSYKLISKQVASDHTYFARYLDG<EHLL<TITHAPRLCVNNGYK<V*HYTSSILHE*DVSP

Parental  NAELWQVSWQPFLDGIFPAKTITYQAVPSEVPNEEPKVATAYRPPALRNKPITNSKLHEEEPPQNMKPQS
          N.E..QVSWQPFLD..FPAK..TYQAVPSE.PN.EPK.A...R.PALRNK.ITNSKLHEE..PQN.K.Q.
Retrocopy NVEIRQVSWQPFLDELFPAKAVTYQAVPSEIPN*EPKFAMTGRLPALRNKLITNSKLHEEKSPQNKKSQP

Parental  GNDKPLSKTALKNQKKHEAKKAAKQEARSDKSPDLAPTPAPQSTPRNTVSQSISGDPEIDKKIKNLKKKL
          GNDKPLSK.ALKNQ.K..AKKA.KQE.RSDKSPDL.PTP.PQSTP.NTVS..I...P....KI...KK..
Retrocopy GNDKPLSKAALKNQRKYKAKKATKQEVRSDKSPDLTPTPVPQSTP*NTVSVNI-WKP*DRRKIQETKKS-

Parental  KAIEQLKEQAATGKQLEKNQLEKIQKETALLQELEDLEL
          KA.E..K....T..QLEK....KI.K.T.LLQELEDL..
Retrocopy KAAEP*K-NTVTETQLEKQ*VRKI-KDTSLLQELEDLKM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2213 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,