RetrogeneDB ID: retro_nleu_1934

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397317.1:7608053..7608635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PERP
• Ensembl ID: ENSNLEG00000014930
• Aliases: None
• Description: None

Sequence

>retro_nleu_1934
ATCCGCTGCGGCCTGGCCTGCGAGCGCTGCCGCTGGATCCTGACCCTGCTCCTACTCAGCGCCATCGCCTTCGACATCAT
CGCCGTGGCCGGCCGCGGCTGGCTGCAGTCGAGCGACCACGTCCAGACGTCCTCGCTGTGGTGGAGATGTTGTCACGAGG
GCGGCGGCGGCAGCGCGTCCTAAGAGGACGGCTGCCAGAGCCTCAGGGAGTACGCGTGGGGTAGAGCAGCGGCTGCCATG
CTCTTCCGGGGCTTCAGCATCCTGGTGATCTGTTTCATCCTCTCCTTGTTCTTCGTCCTGTGTATACCCCAGATACTTGT
CTTCCTAAGAGTGATTGGAAGTCTCCTTGCCTTGGCTGCTGTGTTCCAGATCATCTCCCTGGTAATTTACCCCGTGAAGT
ACACTCAACCTTCAACCTTCATGCCAACCCCCGCTGTCACTTACATCTATAACTGGGCCTACGGCTTTGGGTGGGCAGCC
ACGATTATCTTCATTGGCTATGCTTCCTTCTGCTGCTGCCTCCCCAGCTAGAAAGATGACCTCCTGGGCAATACCAAGCC
CAGGTACTTCTACACATCCGCC

Alignment

ORF - retro_nleu_1934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.67 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRCGLACERCRWILPLLL-NAIAFDIIALAGRGWLQSS-HIQTSSLWWKCSQEGGGSGSS-EEGCQSLME
          IRCGLACERCRWIL.LLL..AIAFDIIA.AGRGWLQSS.H.QTSSLWW.C..EGGG...S.E.GCQSL.E
Retrocopy IRCGLACERCRWILTLLLLSAIAFDIIAVAGRGWLQSSDHVQTSSLWWRCCHEGGGGSAS*EDGCQSLRE

Parental  YAWGRAAAAMLFCGFIILVICFILS-FFALCGPQMLVFLRVIGGLLALAAVFQIISLVIYPVKYTQ-TFN
          YAWGRAAAAMLF.GF.ILVICFILS.FF.LC.PQ.LVFLRVIG.LLALAAVFQIISLVIYPVKYTQ.TFN
Retrocopy YAWGRAAAAMLFRGFSILVICFILSLFFVLCIPQILVFLRVIGSLLALAAVFQIISLVIYPVKYTQ<TFN

Parental  LHAN-PAVTYIYNWAYGFGWAATIILIGCAFFFCCLPNYEDDLLGNAKPRYFYTSA
          LHAN.PAVTYIYNWAYGFGWAATII.IG.A.F.CCLP...DDLLGN.KPRYFYTSA
Retrocopy LHAN>PAVTYIYNWAYGFGWAATIIFIGYASFCCCLPS*KDDLLGNTKPRYFYTSA

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_1934 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020097	1 retrocopy	retro_btau_165,
Callithrix jacchus	ENSCJAG00000019024	1 retrocopy	retro_cjac_3992,
Homo sapiens	ENSG00000112378	2 retrocopies	retro_hsap_1523, retro_hsap_2901,
Gorilla gorilla	ENSGGOG00000028340	1 retrocopy	retro_ggor_1165,
Macropus eugenii	ENSMEUG00000004872	1 retrocopy	retro_meug_845,
Microcebus murinus	ENSMICG00000013979	1 retrocopy	retro_mmur_353,
Myotis lucifugus	ENSMLUG00000001473	1 retrocopy	retro_mluc_2287,
Macaca mulatta	ENSMMUG00000000997	1 retrocopy	retro_mmul_2156,
Nomascus leucogenys	ENSNLEG00000014930	2 retrocopies	retro_nleu_1934 , retro_nleu_631,
Oryctolagus cuniculus	ENSOCUG00000004238	1 retrocopy	retro_ocun_170,
Otolemur garnettii	ENSOGAG00000011669	1 retrocopy	retro_ogar_631,
Pongo abelii	ENSPPYG00000017043	3 retrocopies	retro_pabe_1267, retro_pabe_2400, retro_pabe_2416,