RetrogeneDB ID: retro_nleu_3106

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL398656.1:2177..3254(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000198211
• Ensembl ID: ENSNLEG00000015940
• Aliases: None
• Description: None

Sequence

>retro_nleu_3106
ATAAGGGAGATCGTGCACATCCAGGCCAGCCAGTGCGGCAACCAGATCGGGGCCAAGTTCTGGGAAGTCATCAGTGATGA
GCATGGCATCGACCCTAGTGGCAACTACGTGGGCGACTCGGACTTGCAGCTGGAGCGGATGAGTGTCTACTACAACGAGG
CCTCTTCTCACAAGTACGTGCCTCGGGCCATTCTGGTTGACCTGGAACCCGGAACCATGGACAGTGTCCGCTCAGGGGCC
TTCGGACATCTTTTCAGGCCTGACAATTTCATCTTTGGTCAGAGTGGGGCCGGCAACAACTGGGCCAAGGGTCACTACAC
GGAGGGTGTGGAGCTGGTGGATTCAGTCCTGGATGTCGTGCAGAAGGAGTGTGAAAACTGCGACTGCCTGCAGGGCTTCC
AGCTGACCCACTCACTGGGGGGCAGCACGGGCTCTGGCATGGGCACGCTGCTCATCAGCAAGGTGCGTGAGGAGTATTCC
GACCGCATCCTGAACACCTTCAGCGTCATGCCCTCGCCCAAGGTGTAAGACACGGTGGTGGAGCCCTACAATGCCGCGCT
GTCCATCCACCAGCTGGTGGAGAATACGGATGAGACCTACTGCAACGACAACGAGGCTGTCTACGACATCTGCTTCCGCA
CCCTCAAGCTGGCCACACCCACCTACGGGGACCTCAACCACTTGGTGTCGACCACCATGAGCAGGGTCACCACCTCCCTG
CGCTTCCCGGGCCAGCTCAACGCTGACCTGCGTAAGCTGGCCGTCAACATGGTGCCCTTCCCCCGTCTGCACTTCTTCAC
GCCCGGCTTCGCCCGCCTCACAGCCCGGGGCAGCCAGCAGTACCGGGCCCTGACCGTGCCCGAGCTCACCCAGCAGATGT
TTGATGCCAAGAACATGATGGCTGCCTGCAACCCACACCACGGCCACCACCTGATGGTGGCCACCGTGTTCCGGGGCCGC
ATGTCCATGAAGGAGGTGGACGAGCAGATGCTGGCCATCCAGAGCAAGAACAGCAGCTACTTCGTGGAGTGGATCCCCAA
CAATGTGAAGGTGGCCGTGTGACATCCCGCCCCGCGG

Alignment

ORF - retro_nleu_3106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.09 %
• Parental protein coverage: 79.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYMGDSNLRLERINFYYNDASSHKYVPRAILVDLEP
          .REIVHIQA.QCGNQIGAKFWEVISDEHGIDPSGNY.GDS.L.LER...YYN.ASSHKYVPRAILVDLEP
Retrocopy IREIVHIQASQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERMSVYYNEASSHKYVPRAILVDLEP

Parental  GTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTHSLG
          GTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEG.ELVDSVLDVV.KECENCDCLQGFQLTHSLG
Retrocopy GTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGVELVDSVLDVVQKECENCDCLQGFQLTHSLG

Parental  GGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSIHQLVENTDETYCIDNEALYDI
          G.TGSGMGTLLISKVREEY.DRI.NTFSV.PSPKV.DTVVEPYNA.LSIHQLVENTDETYC.DNEA.YDI
Retrocopy GSTGSGMGTLLISKVREEYSDRILNTFSVMPSPKV*DTVVEPYNAALSIHQLVENTDETYCNDNEAVYDI

Parental  CFRTLKLATPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQ
          CFRTLKLATPTYGDLNHLVS.TMS.VTTSLRFPGQLNADLRKLAVNMVPFPRLHFF.PGFA.LTARGSQQ
Retrocopy CFRTLKLATPTYGDLNHLVSTTMSRVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFTPGFARLTARGSQQ

Parental  YRALTVPELTQQMFDAKNMMAACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVK
          YRALTVPELTQQMFDAKNMMAAC.P.HG..L.VATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVK
Retrocopy YRALTVPELTQQMFDAKNMMAACNPHHGHHLMVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVK

Parental  VAVCDIPPR
          VAV....PR
Retrocopy VAV*HPAPR

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_3106 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010530	1 retrocopy	retro_cjac_1144,
Homo sapiens	ENSG00000258947	1 retrocopy	retro_hsap_155,
Gorilla gorilla	ENSGGOG00000002192	1 retrocopy	retro_ggor_2364,
Nomascus leucogenys	ENSNLEG00000005348	1 retrocopy	retro_nleu_498,
Nomascus leucogenys	ENSNLEG00000015940	1 retrocopy	retro_nleu_3106 ,