RetrogeneDB ID: retro_nleu_1027

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397279.1:4525832..4526721(+)
• 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_1027
CCTTCCTGCACTGAAGCACCTCTGCAGGACTCAGTGACCAAGGAAGAATCAGAGAAAGAGAAAAACTGCTGTGGAAACCA
AGAAGCAGCTGTGCCCCCGTGCTACAGTGGGAGAGTGCCGAGATGGGGAGAACTGTGTGCCTCTCCACGGAGATTCATGT
GACATGTGTGGACTGCAGGTCCTACATCCCATGGATGCTGCCCAGAGATCACAGCGTATAAAATCGTGCATTGAGGCCCG
TGAGAAGGACATGGAGCTCTCACTTGCTGTGCAGCGCAGCAAGGACTTGGTGTTTGGGATCTGCATGGAGGTGGTCTATG
AGAAAGCAAACCCCAGCGAGTGCCGCTTCGGGATCCTCTCCAACTGCAACCACACCTACTGTCTCAAGTGCATTCGCAAG
TGGAGGAGTGCTAAGCAATTTCAGAGCAAGATTGCCTGCCCAGATTGCCAGATCACATCTAACTTTGTCATTCCAAGTGA
GTCCTGGGTGGAAGAGAAAGAAGAGAAGCAGAAACTCATTCAGAAATACAAGGAGGCGTTGGGCAACAAGGCTTGCAGGT
ATTTTGATGAAGGACGTGGGAGCTGCCCATTTGGAAGGAATTGTTTTTACAAGCATGCGTACCCTGATGGGCTTACAGAG
GAGCCACAGAGACAGAAAGTGGGAACATCAAGCAGAAACTGGGTCCAATGAAGGAACCACTTCTGAGAACTCATTGAGGA
AAGAGATAGCAGCAACCCTTTTGACAATGATGAAGAGGTTGTCACCTTTGAGCTGGGCGAGATGTTGCTTATGCTTTTGG
CTGCAGGTGGGGATGACGAACTGGCAGACTCTGAAGATGAATGGGACTTGTTTCATGATGAGCTGGAAGATTTTTATGAT
TTGGATCTA

Alignment

ORF - retro_nleu_1027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.33 %
• Parental protein coverage: 62.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSCTEAPLQGSVTKEESEKEQ-TAVETKKQLCPYAAVGECRYGENCVYLHGDSCDMCGLQVLHPMDAAQR
          PSCTEAPLQ.SVTKEESEKE..TAVETKKQLCP.A.VGECR.GENCV.LHGDSCDMCGLQVLHPMDAAQR
Retrocopy PSCTEAPLQDSVTKEESEKEK>TAVETKKQLCPRATVGECRDGENCVPLHGDSCDMCGLQVLHPMDAAQR

Parental  SQHIKSCIEAHEKDMELSFAVQRSKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQ
          SQ.IKSCIEA.EKDMELS.AVQRSKD.V.GICMEVVYEKANPSE.RFGILSNCNHTYCLKCIRKWRSAKQ
Retrocopy SQRIKSCIEAREKDMELSLAVQRSKDLVFGICMEVVYEKANPSECRFGILSNCNHTYCLKCIRKWRSAKQ

Parental  FESKIIKSCPECRITSNFVIPSEYWVEEKEEKQKLILKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHAY
          F.SKI...CP.C.ITSNFVIPSE.WVEEKEEKQKLI.KYKEA..NKACRYFDEGRGSCPFG.NCFYKHAY
Retrocopy FQSKI--ACPDCQITSNFVIPSESWVEEKEEKQKLIQKYKEALGNKACRYFDEGRGSCPFGRNCFYKHAY

Parental  PDGRREEPQRQKVGTSSRYRAQRRNHFWELIEERENSNPFDNDEEEVVTFELGEMLLMLLAAGGDDELTD
          PDG..EEPQRQKVGTSSR...Q.RNHF.ELIEER..SNPFDND.EEVVTFELGEMLLMLLAAGGDDEL.D
Retrocopy PDGLTEEPQRQKVGTSSRNWVQ*RNHF*ELIEERDSSNPFDND-EEVVTFELGEMLLMLLAAGGDDELAD

Parental  SEDEWDLFHDELEDFYDLDL
          SEDEWDLFHDELEDFYDLDL
Retrocopy SEDEWDLFHDELEDFYDLDL

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_1027 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 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,