RetrogeneDB ID: retro_nleu_2419

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397353.1:1629221..1630424(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPMK
• Ensembl ID: ENSNLEG00000012319
• Aliases: None
• Description: None

Sequence

>retro_nleu_2419
GGCCCCCCGGAAATGCGGGCCCCACCGGCGATGGAGGCCACCCCTGAGGGCACCCCGCAGCCGGCGGGCGGCAGACTCCG
CTTCCTCAACGGCCAAGTGTCCCTCTCGCATCAGGTGGCCGCACATGTGAACGGGAAGGACAGAGTGGGTATACTGCAAC
ACCCAGATGGCACAGTTTTGAAACAGTTACAACCACCTCCAAGGGGCCCAGGAGAGCTGGAATTCTATAATATGGTTTAC
GCTGCTGACTGTTCTGATGGTGTTCTTCTAGAGCTACGAAAATATTTGCCAAAATACGGCATCCGGTCACCTCCCACTGC
ACCAAACCACGTATACCTAAAACCGGAAGATGTGACCCATAAATTTAATAAGCCCTGTATAATGGATACAAAGATAGGGC
AAAAAAGCTATGATCCTTTTGCCTCATCTGAGAAGATTCAGCAACAGGTCAGCAAGTACTCATTAATGGAAGAGATTGGG
TTGTTGGTGCTTGGCATGAGGGTTTATCATGTTCATTCCGATAGCTATGATGTACAAAACCAGCATTGTGGAAGAAGCTT
AACAAAAGAAACTATAAAGGATGCAGTCTCCGGATTTTTTCATAATGGGTACTGCTTAAGAAAAAGATGCTGTTGCTGCT
AGTATTCAGAAGATTGAGAAAATTCTGCAGTGGTTTGAAAACCAGAAGCAGCTTAACTTTTATGCAAGTTCATTACTACT
GGTTTATGAAAGTTCATCTCAGCCAACCACTACAAAACTGAATGACAGAACTTTGGCAGAAAAGTTTTTGTCCAAAGGAC
AACTGTCAGACACAAAGGTACTAGAGTACAATAATAACTTTCATGTGTTAAGCTCCACGGCGAATGGAAAAATAGAGGCT
TAAGTGCGCAAAAGCTTGTCCAAGGTGTATGCTTGTCACAGGAAGATGTATACAAAAACCATCACAGTCAGACTTCAATG
AAAGTTGAAAATCTGGAGCAAGACAATGGGTGGAAAAGCATGTCACAGGAACATTTAAATGGAAATGTACTTTCCCAACT
GGAAAAACTTTTCTACCGTCTTCCCACTGGTTGCCAAGAGATTGCTGAAGTATAAGTGTGAATGATAGAGTTTGCTCATG
TGTTCCCTAGCAACACAATAGATGAGGGATATATTTATGGGCTAAAGCATTTAATTTCTGTACTTCGAAGTATTTTAGAC
AAC

Alignment

ORF - retro_nleu_2419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.86 %
• Parental protein coverage: 96.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPPEMRTPPAIES-PEGTPQPAGGRLRFLNGCVPLSHQVAGHMYGKDKVGILQHPDGTVLKQLQPPPRGP
          GPPEMR.PPA.E..PEGTPQPAGGRLRFLNG.V.LSHQVA.H..GKD.VGILQHPDGTVLKQLQPPPRGP
Retrocopy GPPEMRAPPAMEATPEGTPQPAGGRLRFLNGQVSLSHQVAAHVNGKDRVGILQHPDGTVLKQLQPPPRGP

Parental  RELEFYNMVYAADCFDGVLLELRKYLPKYYGIWSPPTAPNDLYLKLEDVTHKFNKPCIMDVKIGQKSYDP
          .ELEFYNMVYAADC.DGVLLELRKYLPKY.GI.SPPTAPN..YLK.EDVTHKFNKPCIMD.KIGQKSYDP
Retrocopy GELEFYNMVYAADCSDGVLLELRKYLPKY-GIRSPPTAPNHVYLKPEDVTHKFNKPCIMDTKIGQKSYDP

Parental  FASSEKIQQQVNKYPLMEEIGFLVLGMRVYHVHSDSYETQNQHYGRSLTKETIKDGVSRFFHNGYCLR-K
          FASSEKIQQQV.KY.LMEEIG.LVLGMRVYHVHSDSY..QNQH.GRSLTKETIKD.VS.FFHNGYCLR.K
Retrocopy FASSEKIQQQVSKYSLMEEIGLLVLGMRVYHVHSDSYDVQNQHCGRSLTKETIKDAVSGFFHNGYCLR>K

Parental  DAVAASIQKIEKILQWFENQKQLNFYASSLLFVYEGSSQPTTTKLNDRTLAEKFLSKGQLSDTELLEYNN
          DAVAASIQKIEKILQWFENQKQLNFYASSLL.VYE.SSQPTTTKLNDRTLAEKFLSKGQLSDT..LEYNN
Retrocopy DAVAASIQKIEKILQWFENQKQLNFYASSLLLVYESSSQPTTTKLNDRTLAEKFLSKGQLSDTKVLEYNN

Parental  NFHVLSSTANGKIEASVGKSLSKMYARHRKMYT-KKHHSQTSLKVENLEQGNGWKSMSQEHLNGNVLSQL
          NFHVLSSTANGKIEA.V.KSLSK.YA.HRKMYT.K.HHSQTS.KVENLEQ.NGWKSMSQEHLNGNVLSQL
Retrocopy NFHVLSSTANGKIEA*VRKSLSKVYACHRKMYT<KNHHSQTSMKVENLEQDNGWKSMSQEHLNGNVLSQL

Parental  EKVFYHLPTGCQEIAEVEVRMIDFAHVFPSNTIDEGYVYGLKHLISVLRSILDN
          EK.FY.LPTGCQEIAEV.V.MI.FAHVFPSNTIDEGY.YGLKHLISVLRSILDN
Retrocopy EKLFYRLPTGCQEIAEV*V*MIEFAHVFPSNTIDEGYIYGLKHLISVLRSILDN

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_2419 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000011011	1 retrocopy	retro_apla_14,
Cavia porcellus	ENSCPOG00000000222	1 retrocopy	retro_cpor_369,
Erinaceus europaeus	ENSEEUG00000009958	1 retrocopy	retro_eeur_110,
Homo sapiens	ENSG00000151151	2 retrocopies	retro_hsap_1244, retro_hsap_2032,
Gorilla gorilla	ENSGGOG00000008790	1 retrocopy	retro_ggor_1464,
Myotis lucifugus	ENSMLUG00000015030	1 retrocopy	retro_mluc_518,
Nomascus leucogenys	ENSNLEG00000012319	2 retrocopies	retro_nleu_2419 , retro_nleu_2622,
Pongo abelii	ENSPPYG00000002433	3 retrocopies	retro_pabe_1035, retro_pabe_1086, retro_pabe_1689,
Pan troglodytes	ENSPTRG00000002516	2 retrocopies	retro_ptro_1351, retro_ptro_855,