RetrogeneDB ID: retro_nleu_1437

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397293.1:21547359..21548515(+)
• Located in intron of: ENSNLEG00000004341

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIMKLB
• Ensembl ID: ENSNLEG00000002201
• Aliases: None
• Description: None

Sequence

>retro_nleu_1437
TGTAGTTCTGTGGCTGCCAAGTTGTGGTTTTCGACAGATCATCACATCAGGGAAGACTATCCTCAAAAACAGATTTTACG
AGCATTGAAGGCCAAACGTTGTGAGGAGGAACTGGACTTTAGGGCTGTGGTGATGGATGAGGTGGTGCTGACAATCGAGA
AAGGAAACTTGGGTCTGCGGATCAATGGAGAGCTAATCACTGCCTACCCACAAGTGGTGGTAGTCAGAGTACCAACCCCT
TGGGTGCAAAGTGATAGTGACATCACTGTTTTGTGCCATCTAGAGAAGATGGGATGCCAGTTAGTGAACCGACCTCAAGC
CATCCTGAACTGCGTTAATAAGTTCTGGATATTTCAAGAGTTGGCTGGCCACGGTGTTCCTCTGCCAGATACTTTCTCTT
ATGGTGGCCATGAAAATTTTGCTAAAATGATTGATGAAGCTGAAGTACTGGAGTTCCCAATGGTAGTAAAGAATACGCGG
GGTCACAGAGGTAAAGCCGTTTTCTTGGCTCGAGATGAGCACCATTTGGCTGATCTAAGCCATCTTATTTGCCATGAAGC
ACCATACTTGTTCCAGAAGTATGTTAAAGAGTCACATGGACGGGATGTACATGTCATTGTCATGGGAGACCGTGTGGTTG
GCACCATGTTACATTGTTCAACAGATGGGAGAATGCAGAGCAACTGCTCATTAGGTGGTGTGGGGAATGATGTGCTCATT
GAGTGAACAAGGGAAGCAGCTAGCTATCCAGGTGTCTAATATCCTGGGGACAGATGTGTGTGGCATTGACCTGTTGATGA
AAGATGGCGGCTCCTTCTGTGTCTGTGAGGCCAATGCAAATGTAGGTTTCATCACCTTTGATAAGGCTTGTAATCTAGAT
GTAGCTGGTATCATAGCAGACTATGCCGCCTCCCTTCTACCCTCTGGCTGGCTCACCCGGCGTATGTCCCTGCTCTCTGT
GGTGTCCACTGCCAGTGAGACTAGTGAGCTGGAGCTGGGTCCTCCAGCCAGCACTGCTGTTGACAACATGAGTGCAAGTT
CCGGCTCTGTTGACAGTGACCCTGAAAGCATGGAGCAAGAGCTGCTCACCAAGCTCCCAGGGGGCCTGTTCAACATGAAC
CAGCTGCTAGCCAATGAAATCAAACTACTGGTGGAC

Alignment

ORF - retro_nleu_1437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.97 %
• Parental protein coverage: 99.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CSSVAAKLWFLTDRRIREDYPQKEILRALKAKCCEEELDFRAVVMDEVVLTIEQGNLGLRINGELITAYP
          CSSVAAKLWF.TD..IREDYPQK.ILRALKAK.CEEELDFRAVVMDEVVLTIE.GNLGLRINGELITAYP
Retrocopy CSSVAAKLWFSTDHHIREDYPQKQILRALKAKRCEEELDFRAVVMDEVVLTIEKGNLGLRINGELITAYP

Parental  QVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHENF
          QVVVVRVPTPWVQSDSDITVL.HLEKMGC.L.NRPQAILNCVNKFW.FQELAGHGVPLPDTFSYGGHENF
Retrocopy QVVVVRVPTPWVQSDSDITVLCHLEKMGCQLVNRPQAILNCVNKFWIFQELAGHGVPLPDTFSYGGHENF

Parental  AKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKAPFGLISHLIRHEAPYLFQKYVKESHGRDVRVIVVGG
          AKMIDEAEVLEFPMVVKNTRGHRGKAVFLARD.......SHLI.HEAPYLFQKYVKESHGRDV.VIV.G.
Retrocopy AKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDEHHLADLSHLICHEAPYLFQKYVKESHGRDVHVIVMGD

Parental  RVVGTMLRCSTDGRMQSNCSLGGV-GMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKDDGSFCVCEANA
          RVVGTML.CSTDGRMQSNCSLGGV.GMMCSLSEQGKQLAIQVSNILG.DVCGIDLLMKD.GSFCVCEANA
Retrocopy RVVGTMLHCSTDGRMQSNCSLGGV>GMMCSLSEQGKQLAIQVSNILGTDVCGIDLLMKDGGSFCVCEANA

Parental  NVGFIAFDKACNLDVAGIIADYAASLLPSGRLTRRMSLLSVVSTASETSEPELGPPASTAVDNMSASSSS
          NVGFI.FDKACNLDVAGIIADYAASLLPSG.LTRRMSLLSVVSTASETSE.ELGPPASTAVDNMSASS.S
Retrocopy NVGFITFDKACNLDVAGIIADYAASLLPSGWLTRRMSLLSVVSTASETSELELGPPASTAVDNMSASSGS

Parental  VDSDPESTERELLTKLPGGLFNMNQLLANEIKLLVD
          VDSDPES.E.ELLTKLPGGLFNMNQLLANEIKLLVD
Retrocopy VDSDPESMEQELLTKLPGGLFNMNQLLANEIKLLVD

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_1437 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000000332	1 retrocopy	retro_ggor_31,
Nomascus leucogenys	ENSNLEG00000002201	2 retrocopies	retro_nleu_1422, retro_nleu_1437 ,
Rattus norvegicus	ENSRNOG00000023814	1 retrocopy	retro_rnor_255,