RetrogeneDB ID: retro_nleu_2629

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397384.1:1798088..1798605(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC59
• Ensembl ID: ENSNLEG00000009066
• Aliases: None
• Description: None

Sequence

>retro_nleu_2629
GTCAGCTTTGCTCAGCTGAAGAACCTGAAGTGGTTGGACCTGAAGGTTAACCTCTGGATCCCGGCCTGGCCAAGGTGGCA
GGTGACTGGTTGGGTGAGAAGCCAGGGAAACAGCATGCAAACAAGGCATCACAGCACATGAAGACCGTGCACGCAGACCA
CGAGCAGGAGAGGCAGCGGGGCTGTGAGTAGAACTAGAGGTGGAGGAGAAGCATGAGGCAAAGCAGCAAGCTAAGGAAGC
TCAGGAGAGGAAACTGCGGAAGGGGGAGAAGGCAGAAGAGAAAGAGTGCCGGAGAAAGGAGTATGATGCCCTCAAAGCAG
CCAAGCGGGAGCAGATGAAACTTAGGAAGGAAACAAATTAGGCCCCGAAATTTAAGTCCGAATCCTGCCCTGGCAAGCCA
CTCCCCTGGAAGCACACTCATTTCTGTGCTGTGCTGAAGCTGCTGCTGCAGCTGCTGCTGTCTTGTGCGGCAGGAGGGCT
GGTGGCTTGTCGGGTGACAGCTACAGCAGCAGCCCCT

Alignment

ORF - retro_nleu_2629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.48 %
• Parental protein coverage: 56.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSFAQLKNLKWLDLKDN-PLDPVLAKVAGDCLDEKQCKQCANKVLQHMKAVQADQERERQRRLE-VEREA
          VSFAQLKNLKWLDLK.N.PLDP.LAKVAGD.L.EK..KQ.ANK..QHMK.V.AD.E.ERQR..E.VE.E.
Retrocopy VSFAQLKNLKWLDLKVN<PLDPGLAKVAGDWLGEKPGKQHANKASQHMKTVHADHEQERQRGCE<VELEV

Parental  EKKREAKQRAKEAQERELRKREKAEEKERRRKEYDALKAAKREQEKKPKKEANQAPKSKSGSRPRKPPPR
          E.K.EAKQ.AKEAQER.LRK.EKAEEKE.RRKEYDALKAAKREQ..K..KE.N.APK.KS.S.P.KP.P.
Retrocopy EEKHEAKQQAKEAQERKLRKGEKAEEKECRRKEYDALKAAKREQ-MKLRKETN*APKFKSESCPGKPLPW

Parental  KHTRSWAVLKLLLLLLLFGVAGGLVACRVTELQQQP
          KHT.................AGGLVACRVT.....P
Retrocopy KHTHXXXXXXXXXXXXXSCAAGGLVACRVTATAAAP

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_2629 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018827	1 retrocopy	retro_cjac_2342,
Equus caballus	ENSECAG00000018072	1 retrocopy	retro_ecab_240,
Homo sapiens	ENSG00000108829	1 retrocopy	retro_hsap_3479,
Gorilla gorilla	ENSGGOG00000006310	1 retrocopy	retro_ggor_2346,
Monodelphis domestica	ENSMODG00000020901	1 retrocopy	retro_mdom_1882,
Nomascus leucogenys	ENSNLEG00000009066	1 retrocopy	retro_nleu_2629 ,
Pongo abelii	ENSPPYG00000008284	3 retrocopies	retro_pabe_2687, retro_pabe_2874, retro_pabe_2875,
Pan troglodytes	ENSPTRG00000009398	1 retrocopy	retro_ptro_2985,
Tarsius syrichta	ENSTSYG00000000371	1 retrocopy	retro_tsyr_25,
Tursiops truncatus	ENSTTRG00000000207	1 retrocopy	retro_ttru_1931,