RetrogeneDB ID: retro_nleu_1443

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397293.1:14467886..14468550(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THUMPD1
• Ensembl ID: ENSNLEG00000012369
• Aliases: None
• Description: None

Sequence

>retro_nleu_1443
GGACGCCAACAGCAGTGGAGAAACATCTCTCTTTCCTCTCAGCGTGCACACATCATGGCGGCTGCCGCCCGGCAGCCTCC
TCAGCCTGGCGGCGGGAAGCACAGAGGCAAGGCTCAGTATGTGCTGGCCAAGCGAGCTCGGCGCTGCGAATCTGGCAGGC
CCGGTCAGCCAGAGCCCAGGCTATGGGGCATCCTCATCACCTGCAACATGAACCAGCGCCAAGTGTGTGGAGGAGGCCTA
CACCCTGCTCAACGAATATGGCGACATGTACGGGCCAGAAAAGTTTACAGACAAGGATCAGCAGCCCTTTGGAAGTGAGG
GAGATGATGATGATGTGGAGGCTGCCTTGAAGAAAGAAGTTGGTGACATTAAGGCATTCACAGAGATGAGCCTAAGAGGA
TTCCAGTCAGTGGAAAGTGGAGCAAATAACGTCTTCTTCATCAGGACACTTGGGATGGAACTTGAGAAATTGGCGCATCA
TATTCTCCAGGATGTGTACAAAACCAAGAAGACTTGAGTTATTCTATGAATGTTATGCATCTCAGGCACATGCAAGGCTT
TTTTAGAAGATATGAAAAAATACACAGAAACATTTTTGGAACCTTGGTTTAAAGCTCCAAACAAAGGCACATTTCAGATT
GTGTATAAATCTTGAAATAGCAGT

Alignment

ORF - retro_nleu_1443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 51.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRQQQRRNVSLFSQLARTMAAPAQQTTQPGGGKRKCKAQYVLAKRARRCDAGGPRQLEPGLQGILITCNM
          GRQQQ.RN.SL.SQ.A..MAA.A.Q..QPGGGK...KAQYVLAKRARRC..G.P.Q.EP.L.GILITCNM
Retrocopy GRQQQWRNISLSSQRAHIMAAAARQPPQPGGGKHRGKAQYVLAKRARRCESGRPGQPEPRLWGILITCNM

Parental  NER-KCVEEAYSLLNEYGDDMYGPEKFTDKDQQPSGSEGEEDDAEAALKKEVDDIKASTEMRLRRFQSVE
          N.R.KCVEEAY.LLNEYG.DMYGPEKFTDKDQQP.GSEG..DD.EAALKKEV.DIKA.TEM.LR.FQSVE
Retrocopy NQR>KCVEEAYTLLNEYG-DMYGPEKFTDKDQQPFGSEGDDDDVEAALKKEVGDIKAFTEMSLRGFQSVE

Parental  SGANNVVFIRTLGIEPEKLVHHILQDMYKTKKKKTRVILRMLPISGTCKAFLEDMKKYAETFLEPWFKAP
          SGANNV.FIRTLG.E.EKL.HHILQD.YKT..KKT.VIL.ML.ISGTCKAFLEDMKKY.ETFLEPWFKAP
Retrocopy SGANNVFFIRTLGMELEKLAHHILQDVYKT--KKT*VIL*MLCISGTCKAFLEDMKKYTETFLEPWFKAP

Parental  NKGTFQIVYKSRNNS
          NKGTFQIVYKS.N.S
Retrocopy NKGTFQIVYKS*NSS

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_1443 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009499	1 retrocopy	retro_cjac_915,
Cavia porcellus	ENSCPOG00000008919	1 retrocopy	retro_cpor_71,
Felis catus	ENSFCAG00000015158	1 retrocopy	retro_fcat_195,
Homo sapiens	ENSG00000066654	1 retrocopy	retro_hsap_2521,
Gorilla gorilla	ENSGGOG00000005231	1 retrocopy	retro_ggor_1573,
Macaca mulatta	ENSMMUG00000004225	1 retrocopy	retro_mmul_1599,
Monodelphis domestica	ENSMODG00000006971	1 retrocopy	retro_mdom_54,
Nomascus leucogenys	ENSNLEG00000012369	1 retrocopy	retro_nleu_1443 ,
Pan troglodytes	ENSPTRG00000007848	1 retrocopy	retro_ptro_1466,