RetrogeneDB ID: retro_nleu_1757

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397307.1:1346867..1347405(-)
• Located in intron of: ENSNLEG00000011260

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN2
• Ensembl ID: ENSNLEG00000001161
• Aliases: None
• Description: None

Sequence

>retro_nleu_1757
AAGGCCAAGACTAAGGGGCCGCAGAGCGGGGTAGACATTGGCATCAAGTACTCAGAGAAGCAGGAGCAGAACTTCAGTGA
TGCCGCCATGAAGGCTGGCCAGTGCGTCATCGGGCTGCAGATGGGCACCAACAAATGTGCCAGCCAGTTGGGCATGACCG
TGTATGGCGTGAGGAGGCATCTGTGTGACCCCAAGAATCACATCCTGCCCCCCATGGACCACTCGACCATTAGCCTCCAG
ATGGGTACAAATAAGTGTGCCAGCCAGGTGAGCATGACGGCTCCTGGGACGTGGTGGCACATCTATGACACCAAGCTGGG
AACCGACAAGTGTGATAATTCCTCCATGTCCCTGCAGATGGGCTACACCCAGGGTACCAACCATAGTAGCCAGGCCTTTG
GTCTGGGCCAGCATATATATGACCCGAAGTACTGCCCGCCAGGCACAATGGCCGACAGGGCTCCCTTGGGTGCTGGCGAC
TGCCTGGGCCCAGGAGAGGTCCCTGAATATCCCCCCTTACTACCAGGAGGAGGCTGGC

Alignment

ORF - retro_nleu_1757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.44 %
• Parental protein coverage: 75.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QAKTKGLQSGVDIGVKYSEKQERNFDDATMKAGQCVIGLQMGTNKCASQSGMTAYGTRRHLYDPKNHILP
          .AKTKG.QSGVDIG.KYSEKQE.NF.DA.MKAGQCVIGLQMGTNKCASQ.GMT.YG.RRHL.DPKNHILP
Retrocopy KAKTKGPQSGVDIGIKYSEKQEQNFSDAAMKAGQCVIGLQMGTNKCASQLGMTVYGVRRHLCDPKNHILP

Parental  PMDHSTISLQMGTNKCASQVGMTAPGTRRHIYDTKLGTDKCDNSSMSLQMGYTQGANQSGQVFGLGRQIY
          PMDHSTISLQMGTNKCASQV.MTAPGT..HIYDTKLGTDKCDNSSMSLQMGYTQG.N.S.Q.FGLG..IY
Retrocopy PMDHSTISLQMGTNKCASQVSMTAPGTWWHIYDTKLGTDKCDNSSMSLQMGYTQGTNHSSQAFGLGQHIY

Parental  DPKYCPQGTVADGAPSGTGDCPDPGEVPEY-PPYYQEGAG
          DPKYCP.GT.AD.AP.G.GDC..PGEVPEY.PPYYQE.AG
Retrocopy DPKYCPPGTMADRAPLGAGDCLGPGEVPEY>PPYYQEEAG

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_1757 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 10 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000001141	1 retrocopy	retro_dord_672,
Erinaceus europaeus	ENSEEUG00000015171	1 retrocopy	retro_eeur_581,
Gorilla gorilla	ENSGGOG00000028153	9 retrocopies	retro_ggor_1199, retro_ggor_1271, retro_ggor_1555, retro_ggor_1612, retro_ggor_1646, retro_ggor_1922, retro_ggor_2370, retro_ggor_305, retro_ggor_762,
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131,
Nomascus leucogenys	ENSNLEG00000001161	2 retrocopies	retro_nleu_1757 , retro_nleu_2893,
Nomascus leucogenys	ENSNLEG00000011207	5 retrocopies	retro_nleu_122, retro_nleu_1342, retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Nomascus leucogenys	ENSNLEG00000013350	1 retrocopy	retro_nleu_575,
Otolemur garnettii	ENSOGAG00000010144	2 retrocopies	retro_ogar_1416, retro_ogar_1733,
Pongo abelii	ENSPPYG00000009302	12 retrocopies	retro_pabe_1299, retro_pabe_1397, retro_pabe_1838, retro_pabe_1920, retro_pabe_2171, retro_pabe_2249, retro_pabe_2900, retro_pabe_3512, retro_pabe_3515, retro_pabe_3543, retro_pabe_3823, retro_pabe_407,
Ictidomys tridecemlineatus	ENSSTOG00000028367	1 retrocopy	retro_itri_326,