RetrogeneDB ID: retro_nleu_2000

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397321.1:9887260..9888883(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSNLEG00000004777
• Aliases: None
• Description: None

Sequence

>retro_nleu_2000
ATGAAGCAGGTCATTGAGCTGAAAGAGAAGGGCAACAAGGCCCTGGGCACGGGCAACATGGACAATGCCTTACAGTACTA
CTCCGAAGCCATTAAGCTGGATCCCCACAACCACGTGCTCTACAGCAACTGTTCTGCCACCTATGCCAAGAAAGGAGACT
ACCAGAAGGCTTACAAGAATGGCTGCAAGACCGTCGACCTAAAAGCTTGACTGGGGCAAGGGCTATTCACGAAAAGCAGC
AGCTCTAGCATTCTTAAACAGATTTGAAGAAGCCAAGCGAACCTACAAGGAGTGCTTAAAACACAAAGCAAATAACCCTC
AACCGAAAGAGGGTTTACAGAATATGGAGGCCAGGTTGGCAGAGAGAAAATTTATGAATGCTTTCAACATGCCCAATCGG
TATCAGAAGTTGGAGAGTGATCCCAGAACAAGGACACTGCTCAGCGATCCTACCTACTGGGAGCTGATAGAGCAACTACA
AAACAAGCCTTCTGATCTGGGCACAAAACTACAAGATCCCCGGATCATGACCACTCTCAGTGTACTCCTTGAGGTCGATC
TGGGCAGTATGGATGAGGAGGAAGAGATTGCAACACCTTCACCACCACCCCTTCCCAAAAAGGAGACCAAGCCAGAGCCA
ATGGAAGATCTTCCAGACAATAAGAAGCAGGCACTGAAAGAAAAAGAGCTCAGGAATGATGCCTACAAGAAGAAAGACTG
ACACAGCCTTGAAGCATTACAACAAAGCCAAGGAGCTGGACCCCAGCAACATAACTTACATTACCAATCAAGCAGCGGTA
TACTTTGAAAAGGGCAACTACAATAAGTGCCAGAGCTTTGTGAGAAGTCCATTGAAGTGGGGAGAGAAAACAGAGAAGAC
TATCTACAGATTGCCAAAGTGTATGCTCGAATTGGCAACTCCTACTTCAAAGAAGAAAAGTAAAAGGATGCCATCCATTT
CTATAACAAGTATCTGGCAGAGCACCGAACTCCAGATGTGCTCAAGAAATGCCAGCAGGCAGAGAAAATCCTGAAGGAGC
AAGAACGGCTGGCATACATAAACCCCGACCTGGCTTTGGAGGAGAAGAACAAAGGCAATGAGTGTTTTCAGAAAGGGGAC
TATCCCCACGCTGTGTAGCATTATACAGAAGCCATCAAAAGAAACCCAAAAGATGCCAAATTATACAACAATCGAGCTGC
CTGTTACACCAAACTCCTGGATTCCAGCTGGTACTCAAGGACTGTGAGGAATGTATCCAGCTGGAGCCGACCTTCATCAA
GGGTTATACACGGAAAGCCGCTGCTCTGGAAGCGATGAAGGACTACACCAAAGCCATGGATGTGTACCAGAAGGTGCTAG
ACCTGGACTCCAGCTGTAAGGAGGCGGCAGACCGCGATCAACGCTGTATGATGGCGCAGTACAACCGGCACCACAGCCCC
GAAGATGTGAAGCGATGAGCCATGGCAGACCCCGAAGTGCAGCAGATCATGAGTGACACAGCTATGCACCTTATCCTGGA
ACAGATGCAGAAGGACCCCCAGGCACTCAGCATACACTTACAGAATCCTGTAATCGCACAGAAGACCCAGAAGCTGATGG
ATGTGGGTCTGATTGCAATTCGG

Alignment

ORF - retro_nleu_2000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEQVSELKEKGNKALSAGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQK-YEDGCKTVDLKP-
          M.QV.ELKEKGNKAL..GN.D.ALQ.YSEAIKLDPHNHVLYSN.SA.YAKKGDYQK.Y..GCKTVDLK..
Retrocopy MKQVIELKEKGNKALGTGNMDNALQYYSEAIKLDPHNHVLYSNCSATYAKKGDYQKAYKNGCKTVDLKA>

Parental  DWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEARLAERKFMNPFNMPNLYQKLES
          DWGKGYSRKAAAL.FLNRFEEAKRTY.E.LKH.ANNPQ.KEGLQNMEARLAERKFMN.FNMPN.YQKLES
Retrocopy DWGKGYSRKAAALAFLNRFEEAKRTYKECLKHKANNPQPKEGLQNMEARLAERKFMNAFNMPNRYQKLES

Parental  DPRTRTLLSDPTYRELIEQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDEEEEVATPPPPPPPKKET
          DPRTRTLLSDPTY.ELIEQL.NKPSDLGTKLQDPRIMTTLSVLL.VDLGSMDEEEE.ATP.PPP.PKKET
Retrocopy DPRTRTLLSDPTYWELIEQLQNKPSDLGTKLQDPRIMTTLSVLLEVDLGSMDEEEEIATPSPPPLPKKET

Parental  KPEPMEEDLPENKKQALKE-KELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKC
          KPEPME.DLP.NKKQALKE.K..G......K..DTALKHY.KAKELDP.N.TYITNQAAVYFEKG.YNKC
Retrocopy KPEPME-DLPDNKKQALKE>KSSGMMPTRRKT-DTALKHYNKAKELDPSNITYITNQAAVYFEKGNYNKC

Parental  R-ELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKFLAEPRTPDVLKKCQQAEKILK
          ..ELCEK.IEVGRENREDY.QIAK.YARIGNSYFKEEK.KDAIHFYNK.LAE.RTPDVLKKCQQAEKILK
Retrocopy Q<ELCEKSIEVGRENREDYLQIAKVYARIGNSYFKEEK*KDAIHFYNKYLAEHRTPDVLKKCQQAEKILK

Parental  EQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLE-FQLALKD
          EQERLAYINPDLALEEKNKGNECFQKGDYP.A..HYTEAIKRNPKDAKLY.NRAACYTKLL..FQL.LKD
Retrocopy EQERLAYINPDLALEEKNKGNECFQKGDYPHAV*HYTEAIKRNPKDAKLYNNRAACYTKLLD<FQLVLKD

Parental  CEECIQLEPTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYNRHDSPEDVK
          CEECIQLEPTFIKGYTRKAAALEAMKDYTKAMDVYQK.LDLDSSCKEAAD..QRCMMAQYNRH.SPEDVK
Retrocopy CEECIQLEPTFIKGYTRKAAALEAMKDYTKAMDVYQKVLDLDSSCKEAADRDQRCMMAQYNRHHSPEDVK

Parental  RRAMADPEVQQIMSDPAMRLILEQMQKDPQALSEHLKNPVIAQKIQKLMDVGLIAIR
          R.AMADPEVQQIMSD.AM.LILEQMQKDPQALS.HL.NPVIAQK.QKLMDVGLIAIR
Retrocopy R*AMADPEVQQIMSDTAMHLILEQMQKDPQALSIHLQNPVIAQKTQKLMDVGLIAIR

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_2000 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015663	2 retrocopies	retro_btau_836, retro_btau_913,
Canis familiaris	ENSCAFG00000014672	6 retrocopies	retro_cfam_1077, retro_cfam_1172, retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus	ENSCJAG00000018209	2 retrocopies	retro_cjac_1043, retro_cjac_2222,
Cavia porcellus	ENSCPOG00000002914	1 retrocopy	retro_cpor_1443,
Felis catus	ENSFCAG00000005937	1 retrocopy	retro_fcat_1510,
Homo sapiens	ENSG00000168439	1 retrocopy	retro_hsap_4867,
Gorilla gorilla	ENSGGOG00000012132	1 retrocopy	retro_ggor_3040,
Microcebus murinus	ENSMICG00000016933	1 retrocopy	retro_mmur_1045,
Macaca mulatta	ENSMMUG00000012953	1 retrocopy	retro_mmul_2607,
Nomascus leucogenys	ENSNLEG00000004777	1 retrocopy	retro_nleu_2000 ,
Pan troglodytes	ENSPTRG00000003820	1 retrocopy	retro_ptro_3242,
Rattus norvegicus	ENSRNOG00000021164	2 retrocopies	retro_rnor_2862, retro_rnor_468,
Ictidomys tridecemlineatus	ENSSTOG00000014262	1 retrocopy	retro_itri_1578,
Tursiops truncatus	ENSTTRG00000010235	1 retrocopy	retro_ttru_1900,