RetrogeneDB ID: retro_nleu_1029

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397279.1:6519828..6520221(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME2
• Ensembl ID: ENSNLEG00000007919
• Aliases: None
• Description: Nucleoside diphosphate kinase [Source:UniProtKB/TrEMBL;Acc:G1R8Y6]

Sequence

>retro_nleu_1029
ACCATGGCCAACCGAAGTGCACCTTCATCGCCATAAAAGCCAGACAGTGTGCAGCGTGGCCTGGCTGGCAAGATCATGAA
GTGCTTTGAACAGAAGAGATTCCACCTCGTGGCCATGAAGTTCCTCTGGGTCTCTGAGAACATCTGAAGCAGCACTACAT
TCACTGGAAAGACTGCCCATTCTTCCCGAGGCTGGTGAAATAACAGGAACTCAGGGCCTGTCTTACCCATGGTCTGGGAG
GGGCTGAATGCGGTGAAGACAGGCTGAGTGATGGTTGGGGAGACCAATCCAGTGGATTCTAAGCCACACACCATTTGCGG
GGACTTCTCTATTCAGGTGGGCTGATGCATCATTCATGGCAATGGCTCAGTAGTAAGTGCTGAAAAAGAAATC

Alignment

ORF - retro_nleu_1029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 74.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TMANCER-TFIAIK-PDGVQRGLVGEIIKRFEQKGFRLVGLKFMQASEDL-LKEHYVDLKDRPFFAGLVK
          TMAN....TFIAIK.PD.VQRGL.G.I.K.FEQK.F.LV..KF...SE...LK.HY...KD.PFF..LVK
Retrocopy TMANRSA<TFIAIK>PDSVQRGLAGKIMKCFEQKRFHLVAMKFLWVSENI<LKQHYIHWKDCPFFPRLVK

Parental  -YMHSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEI
          ....SGPV..MVWEGLN.VKTG.VM.GETNP.DSKP.TI.GDF.IQVG..IIHG..SV.SAEKEI
Retrocopy >NRNSGPVLPMVWEGLNAVKTG*VMVGETNPVDSKPHTICGDFSIQVG*CIIHGNGSVVSAEKEI

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_1029 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 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004651	1 retrocopy	retro_btau_1707,
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Gorilla gorilla	ENSGGOG00000016526	1 retrocopy	retro_ggor_71,
Monodelphis domestica	ENSMODG00000028492	1 retrocopy	retro_mdom_503,
Mustela putorius furo	ENSMPUG00000015559	5 retrocopies	retro_mputfur_1093, retro_mputfur_1357, retro_mputfur_442, retro_mputfur_667, retro_mputfur_997,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,
Nomascus leucogenys	ENSNLEG00000007919	2 retrocopies	retro_nleu_1029 , retro_nleu_1030,
Nomascus leucogenys	ENSNLEG00000008068	1 retrocopy	retro_nleu_2719,
Oryctolagus cuniculus	ENSOCUG00000022135	1 retrocopy	retro_ocun_1728,
Pan troglodytes	ENSPTRG00000009415	1 retrocopy	retro_ptro_91,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600, retro_rnor_704,