RetrogeneDB ID: retro_nleu_1134

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:9372623..9373267(-)
• 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_1134
CATACTGCAGACAAGCCATATGTTTGTGCAGCTAGTAGCCGTGATCTAAAAACTCAACACAAAATCAAACTTGAAGAGAC
ATTTTACAGGCAAACATGAAAACCAGCAAAAAAAAATACACATATGCAATTCTGAAGGTTGGAAGAAGACCTTTACAAAC
ATCAGCAGCTGAAAAACCATCACTGCCAGCATACTAATGAACCACTATTCAACTGTACCCAGGAAAGATGTGGGAAGCAT
TTTTCCCCATCCATCCAGCAAGCAGCAAGGCCCATGAGGGCTCTATATGTCAAAAAGCGTGTTATTTTGTGGTGAAAGCA
TGAACAGAAGTTTTGAAACATGTGAGAGAAACCTATAAAAAGGAAACAACATATGAAGCAGGCCAGAAAACATTTAAACA
TTATCTTAAGCAACATATGAACACTCATGCTCCAGAAAGGGATATTTTTGACATACAAGAGAAGTCTCTGGAAGAAACCT
ACGCAACTGTGTTTATTCTACAAATCCACATCCTTTCCATGAGAAAAAAGGTGCCATTTTGCATGTGAACATGTTGGCTG
TGGCAAAACATGTGCAATGAAACAAAGTCTTTCTAGGCATGCCGTCGTACATATTCCAACAAGAAGAAAATGAAGCTCAG
AGTA

Alignment

ORF - retro_nleu_1134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.67 %
• Parental protein coverage: 60.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HTGEKPFVCAANGCDQK-FNTKSNLKKHFERKHENQQKQ-YICSFEDCKKTFK-KHQQLKIHQCQHTNEP
          HT..KP.VCAA...D.K..NTKSNLK.HF..KHENQ.....IC..E..KKTF..KHQQLK.H.CQHTNEP
Retrocopy HTADKPYVCAASSRDLK>LNTKSNLKRHFTGKHENQXXXXHICNSEGWKKTFT<KHQQLKNHHCQHTNEP

Parental  LFKCTQEGCGKHFASPSKLKRHAK-AHEGYVCQKGCSFVAKTWTELLKHVRETHKEEILCEVCRKTFKRK
          LF.CTQE.CGKHF.SPS.....A..AHEG..CQK.C.FV.K..TE.LKHVRET.K.E...E...KTFK..
Retrocopy LFNCTQERCGKHF-SPS-IQQAAR<AHEGSICQKACYFVVKA*TEVLKHVRETYKKETTYEAGQKTFKH-

Parental  DYLKQHMKTHAPERDVCRCPREGCGRTYTTVFNLQSHILSFHEESRPF-VCEHAGCGKTFAMKQSLTRHA
          .YLKQHM.THAPERD...........TY.TVF.LQ.HILS......PF..CEH.GCGKT.AMKQSL.RHA
Retrocopy -YLKQHMNTHAPERDIFDIQEKSLEETYATVFILQIHILSMRKKV-PF>ACEHVGCGKTCAMKQSLSRHA

Parental  VVHDP-DKKKMKLKV
          VVH.P..KKKMKL.V
Retrocopy VVHIP<NKKKMKLRV

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_1134 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,