RetrogeneDB ID: retro_nleu_531

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:707578..708260(+)
• Located in intron of: ENSNLEG00000000578

Retrocopy information

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

Parental gene information

• Parental gene symbol: F3
• Ensembl ID: ENSNLEG00000011112
• Aliases: None
• Description: Tissue factor [Source:UniProtKB/TrEMBL;Acc:G1RJV1]

Sequence

>retro_nleu_531
CTGGCGACTCCAGCCTGGGCCTGGGTCCCACGTCCTGAGACTGCCTTAGCTGAGATGCTCCTGCTCTGCCAGGTCCTCCT
CAAGGCAGCTAGTGCTTCTGGCATTGCAGATAGAGTGGTAGCATATAATGTATAATCAATGAATTTCAAGACAATTTTGG
AGCTGAAACCCAAGCCTATCAATCATGTCTACACTGCTCAGACAAGCTCTGCATCAGGAGACCGGAAAAGCCATGCTTGG
AAACCCTGGACACAGAGAGCGACCTCAAAGATGGGACAGCAAGGACGTGACACAGATGTCCTTGGCCCAGGGCCCTTCCT
GCCCCGCTGGGGATGCAGCCACCACGGGTTCTGCTGGGAACCTCTGATCCGAAGCTCACCAGAGTTTACATGTGACCTGG
AGACACACCTCGGACAGCCAACAATTCAGTGTTTTGAATCAGTCGGGACAAAACAACGTGCCAGTATCAGAATGACGTAC
CTTAGAAAGAATGACATATTCCTAGGCCTCTGGGAGTTTGCGACAAGTACTTAAGTTATACACTTTATTATTGGAAAGCT
TCATGTACGGGAAGGAAAACAGCCAAGACAAACACAAATGCGTTTTTGATGGATATGGATAAAGGGGAAACCACCGTTCC
AATGTTCAAGCAGTGTTTCCATCCGAAGACTACACAAGACGA

Alignment

ORF - retro_nleu_531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.88 %
• Parental protein coverage: 78.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  METPAWPRVPRPETAVARTLLLGWVFAQVAGASGTTNTVAAYNLTWKSTNFKTILEWEPKLINQVYTVQI
          ..TPAW..VPRPETA.A..LLL..V....A.ASG....V.AYN....S.NFKTILE..PK.IN.VYT.Q.
Retrocopy LATPAWAWVPRPETALAEMLLLCQVLLKAASASGIADRVVAYNV*--SMNFKTILELKPKPINHVYTAQT

Parental  STKSGDWKSK-CFYTTDTECDLTDEIV-KDVKQTYLARVFSYLAGNVESTGSAG-EPLYENSPEFTPYLE
          S..SGD.KS..C..T.DTE.DL.D....KDV.Q..LA...S..AG....TGSAG.EPL...SPEFT..LE
Retrocopy SSASGDRKSH<CLETLDTESDLKDGTA<KDVTQMSLAQGPSCPAGDAATTGSAG<EPLIRSSPEFTCDLE

Parental  TNLGQPTIQSFEQLGTKVNVTVQDEWTLVRSNDTFLSLRD-VFGKDLIYTLYYWKSSSSGKKTAKTNTNE
          T.LGQPTIQ.FE..GTK.........T..R.ND.FL.L...V..K.L.YTLYYWK.S..G.KTAKTNTN.
Retrocopy THLGQPTIQCFESVGTKQRASIR--MTYLRKNDIFLGLWE<VCDKYLSYTLYYWKASCTGRKTAKTNTNA

Parental  FLIDVDKGE-NYCFSVQAVIPSRTANRK
          FL.D.DKGE.N....VQAV.PS....R.
Retrocopy FLMDMDKGE<NHRSNVQAVFPSEDYTRR

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_531 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000117525	1 retrocopy	retro_hsap_3952,
Gorilla gorilla	ENSGGOG00000014683	1 retrocopy	retro_ggor_2655,
Nomascus leucogenys	ENSNLEG00000011112	1 retrocopy	retro_nleu_531 ,
Pongo abelii	ENSPPYG00000001139	2 retrocopies	retro_pabe_3255, retro_pabe_3256,