RetrogeneDB ID: retro_nleu_939

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:23265473..23266832(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSNLEG00000001921
• Aliases: None
• Description: None

Sequence

>retro_nleu_939
TCCCCTACCAGGATCCCCTCAGTCACCATTCTGTCCCCAGGGGGCAGGCGAGGGGGCGGCGGCAGCGATGGCAGCGGCGG
CGGCTGGACTAAACAGGTCACCTGCAGGTATTTTATGCATGGGGTTTGTAAGGAAGGAGATAACTGTTGCTAGTTGCATG
ACCTCTCTGACAGTCCGTATAATGTAGTGTACAAGAGTTTGCAGCGAGGGTACTGTATTTATGGCGACTGCTGCAGATAT
GAACATAGCAAGCCATTGAAACAGGAAGAAGCAACTGCTACAGAGCTAACTACAAAGTCATCCCTTGCCGCTTCCTCAAG
TCTCTCATGGATAGTTGGACCACTTGTTGAAATGAATACGGGTGAAGCTGAGTCAAGAAATTCAAACTTTGTAACTGTAG
GAGCAGGTTCAGAGGGCTGGGTGAATGCTATTGAGTTTGTTCCTGGGCAACCCTACTGTGGCCGCACTGCGCCTTCCTGC
ACTAAAGCACCCCTGTAGGGCTCAGTGACCAAGGAAGAATCAGAGAAAGAGCAAACTGCCGTGGAAACAAAGAAGCAGCT
GTGCCCTTATGCTGCAGTGGGAGAGTGCCGATATCGGGAGAACTTGTGTGTATATGGAGATTCATGTGACGTGTGGCTGC
AGGTCCTGCATCTGATGGATGCTGCCCAGAGATCACAGCATATAAAATCGTGCTTTGAGGCCCATGAGAAGGACATGGAG
CTCTCATTTGCTGTGCAGAGCAGCGAGGAAATGGTGTGTGAGATCTGCATGGAGATGATCTATGAGAAAGCCAACCCCAG
AGAGCACCGCTTCGGGATCCTCTCCAACTGCAACCACATCTACTGTCTTAAGTGCATTCGCAAATGGAGGAGTGCTAAGC
AATTTGGGAGCAAGATCATAAAGTCCTGCCCGGAATGTCGGATCACATCTAACTTTGTAATTCCAAGTGAGTACTGTATG
GAGGAGAAAGAAGAGAAGCAGAAACTCATTCTGAAATACAAGGAGGCAATGAGCAACAAGGCGTGCAGGTATTTTGATGG
ACATGGAAGCTGCCCGTTTGGAGGGAACAGTTTTTATAAGCATGTGTACCCTGATGGCCGTAGAGAGGAGCTACAGAGAC
AGAAAGTGGGAACATCAAGCAGATACCCGGCCCAATGAAGGAACCACTACTGGGAACTCATTGAGGAAAGAGAGAACAGC
AGCCCCTTTGACAATGATGAAGAAGAGGTTGTCACCTTTGAGCTGGGCGAGTTGTTGCTTATGCTTTTGGCTGCAGTTGG
GGACGAGGAACTAACAGACTCTGAAGATGAGTGCAACTTGTTTCATGAGGAGCTGGAAGATTTTTATGACTTGGATCTA

Alignment

ORF - retro_nleu_939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.87 %
• Parental protein coverage: 94.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPTPIPTVTAPSLGAGGGGGGSDGSGGGWTKQVTCRYFMHGVCKEGDNCRYSHDLSDSPCSVVCKYFQRG
          SPT.IP.VT..S.G...GGGGSDGSGGGWTKQVTCRYFMHGVCKEGDNC...HDLSDSP..VV.K..QRG
Retrocopy SPTRIPSVTILSPGGRRGGGGSDGSGGGWTKQVTCRYFMHGVCKEGDNCC*LHDLSDSPYNVVYKSLQRG

Parental  YCIYGDRCRYEHSKPLKQEEAAATELTTKSSLAASSSLSSIAGPLVEMNTGEAESRNSNFATVGAGSEDW
          YCIYGD.CRYEHSKPLKQEEA.ATELTTKSSLAASSSLS.I.GPLVEMNTGEAESRNSNF.TVGAGSE.W
Retrocopy YCIYGDCCRYEHSKPLKQEEATATELTTKSSLAASSSLSWIVGPLVEMNTGEAESRNSNFVTVGAGSEGW

Parental  VNAIEFVPGQPYCGRTAPSCTEAPLQGSVTKEESEKEQTAVETKKQLCPYAAVGECRYGEN-CVYLHGDS
          VNAIEFVPGQPYCGRTAPSCT.APL.GSVTKEESEKEQTAVETKKQLCPYAAVGECRY.EN.CVY..GDS
Retrocopy VNAIEFVPGQPYCGRTAPSCTKAPL*GSVTKEESEKEQTAVETKKQLCPYAAVGECRYRENLCVY--GDS

Parental  CDMCGLQVLHPMDAAQRSQHIKSCIEAHEKDMELSFAVQRSKDMVCGICMEVVYEKANPSERRFGILSNC
          CD...LQVLH.MDAAQRSQHIKSC.EAHEKDMELSFAVQ.S..MVC.ICME..YEKANP.E.RFGILSNC
Retrocopy CDV-WLQVLHLMDAAQRSQHIKSCFEAHEKDMELSFAVQSSEEMVCEICMEMIYEKANPREHRFGILSNC

Parental  NHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFVIPSEYWVEEKEEKQKLILKYKEAMSNKACRYFDE
          NH.YCLKCIRKWRSAKQF.SKIIKSCPECRITSNFVIPSEY..EEKEEKQKLILKYKEAMSNKACRYFD.
Retrocopy NHIYCLKCIRKWRSAKQFGSKIIKSCPECRITSNFVIPSEYCMEEKEEKQKLILKYKEAMSNKACRYFD-

Parental  GRGSCPFGGNCFYKHAYPDGRREEPQRQKVGTSSRYRAQRRNHFWELIEERENSNPFDNDEEEVVTFELG
          G.GSCPFGGN.FYKH.YPDGRREE.QRQKVGTSSRY.AQ.RNH.WELIEERENS.PFDNDEEEVVTFELG
Retrocopy GHGSCPFGGNSFYKHVYPDGRREELQRQKVGTSSRYPAQ*RNHYWELIEERENSSPFDNDEEEVVTFELG

Parental  EMLLMLLAAGGDDELTDSEDEWDLFHDELEDFYDLDL
          E.LLMLLAA.GD.ELTDSEDE..LFH.ELEDFYDLDL
Retrocopy ELLLMLLAAVGDEELTDSEDECNLFHEELEDFYDLDL

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_939 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.

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Choloepus hoffmanni	ENSCHOG00000011015	3 retrocopies	retro_chof_173, retro_chof_2357, retro_chof_89,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Dasypus novemcinctus	ENSDNOG00000019564	2 retrocopies	retro_dnov_1011, retro_dnov_388,
Felis catus	ENSFCAG00000024942	1 retrocopy	retro_fcat_67,
Homo sapiens	ENSG00000133606	4 retrocopies	retro_hsap_1140, retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Microcebus murinus	ENSMICG00000002114	1 retrocopy	retro_mmur_1184,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus	ENSMUSG00000029922	1 retrocopy	retro_mmus_2663,
Nomascus leucogenys	ENSNLEG00000001921	4 retrocopies	retro_nleu_1027, retro_nleu_2167, retro_nleu_33, retro_nleu_939 ,
Otolemur garnettii	ENSOGAG00000009877	2 retrocopies	retro_ogar_3468, retro_ogar_424,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes	ENSPTRG00000019766	5 retrocopies	retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa	ENSSSCG00000016498	2 retrocopies	retro_sscr_43, retro_sscr_637,
Tarsius syrichta	ENSTSYG00000009996	3 retrocopies	retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus	ENSTTRG00000009528	2 retrocopies	retro_ttru_1064, retro_ttru_1128,