RetrogeneDB ID: retro_nleu_482

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397266.1:10266509..10267071(+)
• Located in intron of: ENSNLEG00000013486

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSX1
• Ensembl ID: ENSNLEG00000003504
• Aliases: None
• Description: None

Sequence

>retro_nleu_482
ATGAATGGAGACAGCACCTTTGCAAAGAGACCCAAGGATGATGCTCAGATTATCAGAGAAGAGACACAAGGCCTTCACTG
ATATTGCCAGATACTTATCTAATAAAGAGTGGGAAAAGCTGAGAAACTCAGAGAAAATCATCTATGTGTATATGAAGAGA
AACTATGAGACCATGACTAAACTAGGTCTCCAGGCCACCCTCCCAACTTTCATGTACAATAAATGGGCTGCAGAACTCCA
GGGGAATGATATAGACTAAAACTGTGGGAATCAGGATGAATATCCTCAGATGGCTTTTGGCATGCTACAAGGAAACTTTC
CAAAGATGATGCCCAAGAAGCCAGCAAAGGAAGGAAATGATCGAAGGGAGTGCCAGAAGCACCTGGCTCACAGAACGATG
GGAAACAGCTGTGTCCCCCGGGAAAAGAAATTACCTCTGAGAAGACTAACAAGACATCTGGACCCAAGAAAAGGGGGAAC
ATGTCTGGACTCACAGACTGCAAGAGAGAGAAAGTATCTAGTGATTTAGGAAGAGATCAGCGACCCTGAGGAAGATGACA
AA

Alignment

ORF - retro_nleu_482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNGDDAFASRPRDDAQI-SDKLRKAFDDIAKYFSKNEWEKMKSSEKIIYVYMKRKYEAMTKLGFKVTLPP
          MNGD..FA.RP.DDAQI.S.K..KAF.DIA.Y.S..EWEK...SEKIIYVYMKR.YE.MTKLG...TLP.
Retrocopy MNGDSTFAKRPKDDAQI>SEKRHKAFTDIARYLSNKEWEKLRNSEKIIYVYMKRNYETMTKLGLQATLPT

Parental  FMCSKRAADFQGNDFYNDRNHRNQVERPQTTFGRLQRIFPKIMPKKPAEEGND-SKEVPEASAPQNHGKE
          FM..K.AA..QGND...D.N..NQ.E.PQ..FG.LQ..FPK.MPKKPA.EGND.SK.VPEA...QN.GK.
Retrocopy FMYNKWAAELQGNDI--D*NCGNQDEYPQMAFGMLQGNFPKMMPKKPAKEGND<SKGVPEAPGSQNDGKQ

Parental  LCPPGNPSTSEKIHETSGP-KRGKHAW-THRLRERKQVVIYEEISDPEEDDE
          LCPPG...TSEK...TSGP.KRG.........RERK..VI.EEISDPEEDD.
Retrocopy LCPPGKEITSEKTNKTSGPKKRGNMSG>SQTARERKYLVI*EEISDPEEDDK

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_482 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014776	1 retrocopy	retro_cjac_2373,
Homo sapiens	ENSG00000204645	1 retrocopy	retro_hsap_3512,
Gorilla gorilla	ENSGGOG00000026107	1 retrocopy	retro_ggor_2374,
Nomascus leucogenys	ENSNLEG00000003504	1 retrocopy	retro_nleu_482 ,
Ictidomys tridecemlineatus	ENSSTOG00000015375	3 retrocopies	retro_itri_1394, retro_itri_1855, retro_itri_746,