RetrogeneDB ID: retro_nleu_935

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:14601665..14602283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALA
• Ensembl ID: ENSNLEG00000003055
• Aliases: None
• Description: None

Sequence

>retro_nleu_935
ATGGCCGCAAATAAGCCCAAGGTTCGGAATAATTTGGCCTTACACAAAGTCATCACGGTGGGCAGTGCCGGTGTGGGCAA
GGCAGCTCTGACTCTACAGTTCATGTACGATGAGTTTGTGGAGGACTATGAGCTTATCAAAGAAGGCACCTATCGGAAGA
AACTAGTACTGGATGGCGAGGAAGTACAGATCGAAATCTTAAAAACAGCTGGGCAGGAGGACTATGCTGCAATTAAGGAC
AACTATTTCCGAAGCAGAGAGGGGTTTCTCTGTGTCTTCTCAATTACAGAAATGGAATCCTTTGCAGCTACAGCTGACTT
CAGAGAGCAGATTTTAAGAGTAAAAGAAGATGAGAATGTTCCATTTCTACTGGTTGGTAACAAATCAGATTTAGAAGATA
AAAGGCAGGTTTCTGTAAAAGAGGCAAAAAACAGAGCTGACCAGTGAAATGTTAACTATGTGGAAACATCTGCTGAAACA
CGAGCTAATGTTGACAAGGTATTTTTTGATTTAATGAGAGAAATTCGAGCAAAAAAGATGGAAGACAGCAAACTGAAGAA
TGGAAAAAAGAAGAGGAAAAGTTCAGCCAAGAGAATCAGAGAAAGGTGCTGCATTTTA

Alignment

ORF - retro_nleu_935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAANKPKGQNSLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTA
          MAANKPK..N.LALHKVI.VGS.GVGK.ALTLQFMYDEFVEDYE..K...YRKK.VLDGEEVQI.IL.TA
Retrocopy MAANKPKVRNNLALHKVITVGSAGVGKAALTLQFMYDEFVEDYELIKEGTYRKKLVLDGEEVQIEILKTA

Parental  GQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVE
          GQEDYAAI.DNYFRS.EGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSV.
Retrocopy GQEDYAAIKDNYFRSREGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVK

Parental  EAKNRAEQWNVNYVETSAKTRANVDKVFFDLMREIRARKMEDSKEKNGKKKRKSLAKRIRERCCIL
          EAKNRA.Q.NVNYVETSA.TRANVDKVFFDLMREIRA.KMEDSK.KNGKKKRKS.AKRIRERCCIL
Retrocopy EAKNRADQ*NVNYVETSAETRANVDKVFFDLMREIRAKKMEDSKLKNGKKKRKSSAKRIRERCCIL

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_935 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 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Dasypus novemcinctus	ENSDNOG00000017413	1 retrocopy	retro_dnov_573,
Homo sapiens	ENSG00000006451	2 retrocopies	retro_hsap_1136, retro_hsap_3707,
Macropus eugenii	ENSMEUG00000000259	1 retrocopy	retro_meug_1638,
Macaca mulatta	ENSMMUG00000016059	2 retrocopies	retro_mmul_1706, retro_mmul_882,
Nomascus leucogenys	ENSNLEG00000003055	1 retrocopy	retro_nleu_935 ,
Nomascus leucogenys	ENSNLEG00000003573	2 retrocopies	retro_nleu_1034, retro_nleu_481,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Nomascus leucogenys	ENSNLEG00000005266	1 retrocopy	retro_nleu_338,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes	ENSPTRG00000019108	1 retrocopy	retro_ptro_2511,
Sus scrofa	ENSSSCG00000029741	1 retrocopy	retro_sscr_634,
Ictidomys tridecemlineatus	ENSSTOG00000020292	2 retrocopies	retro_itri_1314, retro_itri_1315,
Vicugna pacos	ENSVPAG00000002810	1 retrocopy	retro_vpac_211,