RetrogeneDB ID: retro_nleu_930

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:5747107..5747884(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TADA2A
• Ensembl ID: ENSNLEG00000002646
• Aliases: None
• Description: None

Sequence

>retro_nleu_930
TGGGACTTGAGAGACATTGATTTTGTTGAAGATGACTCGGACATTTTACATGCTCTGAAGATGGCTGTGGTAGATATCTA
TCATTCCAGGTTAAAGGAGAGACAAAGATGAAAAAAAATTATAAGAGACCATGGATTAATCAACCTTAGAAAGTTTCAAT
TAATGGAACGGCGGTATCCCAAGGAGGTCCATGACCTGTATGAAACAATGAGGCGACTTGCAAGAATCGTGGGGCCAGTG
GAACATGACAAATTCATTGAAAGCCATGCATTGGAATTTGAACTTCGAAGGGAAATCAAGAGGCTCCAAGAATACAGGAC
AGCAGGCATTACCAATTTTTGTAGTGCCATAACCTACGATCACCTCAAGAATACACGGGAGGAAGAGCACCTTAAATGCA
CTATGCTCTCAGAAGTTCTCCAGTATATCCAGGACAGTAGTGCTTGCCAGCAGTGGCTCCGCCGGCAAGCTGACATTGAT
TCCGGCCTGAGTCGTTCCATTCTAATGGCTTCGAATTCAGGTAGACGGAGTGCACCACCCTTGAACCTCACTGGCCTCCC
TGGCACAGAGAAGCTGAATGAAAAAGAAAAGGAGCTCTGTCAGATGGTGAGATTTGTCCCTGGAGCCTATTTAGAATACA
AATCTGCTCTATTGAACGAATGTAACAAGCAAGGAGGCTTAAGACTGGCGCAGGCAAGAGCACTCATCAAGATAGATGTG
AACAAAATCTGGAAAATCTATGACTTCCTCATCCGAGAAGGATACATCACTAAAGGC

Alignment

ORF - retro_nleu_930 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.82 %
• Parental protein coverage: 58.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WDLRDIDFVEDDSDILHALKMAVVDIYHSRLKERQRRKKIIRDHGLINLRKFQLMERRYPKEVQDLYETM
          WDLRDIDFVEDDSDILHALKMAVVDIYHSRLKERQR....IRDHGLINLRKFQLMERRYPKEV.DLYETM
Retrocopy WDLRDIDFVEDDSDILHALKMAVVDIYHSRLKERQRXXXXIRDHGLINLRKFQLMERRYPKEVHDLYETM

Parental  RRFARIVGPVEHDKFIESHALEFELRREIKRLQEYRTAGITNFCSARTYDHLKKTREEERLKRTMLSEVL
          RR.ARIVGPVEHDKFIESHALEFELRREIKRLQEYRTAGITNFCSA.TYDHLK.TREEE.LK.TMLSEVL
Retrocopy RRLARIVGPVEHDKFIESHALEFELRREIKRLQEYRTAGITNFCSAITYDHLKNTREEEHLKCTMLSEVL

Parental  QYIQDSSACQQWLRRQADIDSGVSPSIPMASNSGRRSAPPLNLTGLPGTEKLNEKEKELCQMVRLVPGAY
          QYIQDSSACQQWLRRQADIDSG.S.SI.MASNSGRRSAPPLNLTGLPGTEKLNEKEKELCQMVR.VPGAY
Retrocopy QYIQDSSACQQWLRRQADIDSGLSRSILMASNSGRRSAPPLNLTGLPGTEKLNEKEKELCQMVRFVPGAY

Parental  LEYKSALLNECNKQGGLRLAQARALIKIDVNKTRKIYDFLIREGYITKG
          LEYKSALLNECNKQGGLRLAQARALIKIDVNK..KIYDFLIREGYITKG
Retrocopy LEYKSALLNECNKQGGLRLAQARALIKIDVNKIWKIYDFLIREGYITKG

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_930 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003460	2 retrocopies	retro_chof_15, retro_chof_2113,
Nomascus leucogenys	ENSNLEG00000002646	1 retrocopy	retro_nleu_930 ,