RetrogeneDB ID: retro_nleu_214

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:37389507..37390331(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3A
• Ensembl ID: ENSNLEG00000000331
• Aliases: None
• Description: None

Sequence

>retro_nleu_214
CGCCACATCCTGATTCACATTGGAGAAAAGCCTTTTATTTGTGCAGCTAGTGGCTGTGATAAAAAAAAAAAATCCCACAC
AAAATCCAACTGGAAGAAACATTTTGCATGCAAATATGAAAATCTGCAAAAGCAATATGTATGCAATTTTAAAGGATGTA
AGAAGACCTTTAAGAAGCATCAGCAGCTGAAAATCCATCAGTGCCAGCATGAAAATAAACCCCTATTCAAGTTTTACCTT
GAAGGATGTGGAAAACACTTTGTTTCACCCTGCAGGCTGGGAGGACAGATGCAGGCTCGTCAGAAAATTATATGTCAATA
GGGATGTTCTTTTGTGGCAGAAACATGGACAGAGCTTCCAAAGCACATGAGAGAAATCCATAGAAAGGAAATAACATACG
ATGTATGCCAGAAAACATTCAAATGTGAAGATTATCTCAGATAACCTGTGAAAACTCATGCCTCAGAAAGAGATGTATGT
CAACATCCAAGAGAAGACTGCAGAAGAACTGTATTTAATCTCCAGAGCTGTCTTCTTTCTTTTCATAAGGAGAAGCACCC
ATTTATGTGTGAACATGCTGGCTGTGGCAAAAGGTTGGCTATGAAACAAACTCTTACAAGACATGCTATTGTGTATGAGC
TTGACAGGAAGAAAATGAAGATCAAAGTAAAGCTATCTTCTGAAAAATGAAATTTGGCCTCTCATCTCAGTAAAATATCG
CTCGTAAGAGGAAACAAGAACAAGGTTTATCTTTGCATAAAAATGGAGAGTCATTGAATTGTATTGATCTCGACAGCTTC
AATACTTACTCTCAGCTAAAAATC

Alignment

ORF - retro_nleu_214 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.08 %
• Parental protein coverage: 76.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RHILTHTGEKPFVCAANGCDQKF--NTKSNLKKHFERKHENQQKQYICSFEDCKKTFKKHQQLKIHQCQH
          RHIL.H.GEKPF.CAA.GCD......TKSN.KKHF..K.EN.QKQY.C.F..CKKTFKKHQQLKIHQCQH
Retrocopy RHILIHIGEKPFICAASGCDXXXXSHTKSNWKKHFACKYENLQKQYVCNFKGCKKTFKKHQQLKIHQCQH

Parental  TNEPLFKCTQEGCGKHFASPSKLKRHAKAHEGYVCQKGCSFVAKTWTELLKHVRETHKEEILCEVCRKTF
          .N.PLFK...EGCGKHF.SP..L.....A.....CQ.GCSFVA.TWTEL.KH.RE.H..EI...VC.KTF
Retrocopy ENKPLFKFYLEGCGKHFVSPCRLGGQMQARQKIICQ*GCSFVAETWTELPKHMREIHRKEITYDVCQKTF

Parental  KRKDYLKQHMKTHAPERDVCRCPREGCGRTYTTVFNLQSHILSFHEESRPFVCEHAGCGKTFAMKQSLTR
          K..DYL....KTHA.ERDVC..PRE.C.RT...VFNLQS..LSFH.E..PF.CEHAGCGK..AMKQ.LTR
Retrocopy KCEDYLR*PVKTHASERDVCQHPREDCRRT---VFNLQSCLLSFHKEKHPFMCEHAGCGKRLAMKQTLTR

Parental  HAVVHDPDKKKMKLKVKKSREKRSLASRLSGY-IPPKRKQGQGLSLCQNGESPNCVEDKMLSTVAVLTL
          HA.V...D.KKMK.KVK.S.EK..LAS.LS...I..KRKQ.QGLSL..NGES.NC.......T...L..
Retrocopy HAIVYELDRKKMKIKVKLSSEK*NLASHLSKI<IARKRKQEQGLSLHKNGESLNCIDLDSFNTYSQLKI

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_214 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019373	1 retrocopy	retro_cjac_3066,
Equus caballus	ENSECAG00000014803	1 retrocopy	retro_ecab_866,
Felis catus	ENSFCAG00000006982	1 retrocopy	retro_fcat_426,
Gasterosteus aculeatus	ENSGACG00000003107	1 retrocopy	retro_gacu_6,
Gorilla gorilla	ENSGGOG00000008407	1 retrocopy	retro_ggor_2622,
Microcebus murinus	ENSMICG00000014763	1 retrocopy	retro_mmur_368,
Macaca mulatta	ENSMMUG00000009029	1 retrocopy	retro_mmul_1632,
Nomascus leucogenys	ENSNLEG00000000331	2 retrocopies	retro_nleu_1134, retro_nleu_214 ,
Oreochromis niloticus	ENSONIG00000014134	1 retrocopy	retro_onil_8,
Vicugna pacos	ENSVPAG00000004995	1 retrocopy	retro_vpac_456,