RetrogeneDB ID: retro_nleu_2930

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397490.1:574051..575170(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000007556
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: REXO4
• Ensembl ID: ENSNLEG00000013130
• Aliases: None
• Description: None

Sequence

>retro_nleu_2930
CCAGGAAGCGGCCCCGGTGCTGTGGTGCGACCTCCAAAGGCACCAGAAGACTTTTCTCAAAACTAGAAGGCGCTGCAAGA
GTGGCTGCTGAAACAAAAATCTCAGGCCTCAGAAAAGCCTCTTGTCATCTCTCAGATGGGTTCCAAAAAGAAGCCCAAAA
TTATCCAGCAAAACAAAAAAGAGACCTCGCCTCAAGTGAAGGGAGAGGAGATGCCGGCAGGAAAAGACCAAGAGGCCATC
AGGGGCTCTGTTCCTTCAAGCTCCAAGATGGACAGGAAGGCGCCAGTACCTCGCACCAAAGCCAGTGGAGCAGAGCACAA
TAAGAAAGGAACCAAGGAAAGGACAAATGGTGATATTGTTCCAGAACGAGGGGACATCAAGCATAAGAAGCGGAAAGCTA
AGGAGGCAGTCCCGGCCCCACCCACCGAGGAAGACATCTGGTTTGACGACGTGGACCCGGCGGATATCGAAGCTGCCATA
GGTCCAGAGGCGGCCAAGACAGCGAGGAAACAGGTGGGTCAGAGCGAGGGCAGCGTCAGCCTCAGCCTCATGAAAACGCA
GGCCTTCGGCGGCCTGACAAGAGCCTTAGCCTTGGACTGTGAGATGGTGGGCGTGGGCCCTAAGGGGGAGGAGAGTGTGG
CCGCCCGTGTGTCCATCATGAACCAGTATGGGAAGTGCGTTTATGACAAGTACGTCAAACCAACCGAGCCCGTGACGGAC
TATAGGACAGCGGTCAGTGGGATTCAGCCTAAGAACCTCAAGCAGGGAGAAGAGCTTGAAGTTGTTCAGAAGGAAGTGGT
AGAGACACTGAAGGGCAGAATTCTAGTGGGGCATGCTCTGCATAATGACCTAAAGGTACTGTTTCTTGATCACCCAAAAA
AGAAGATTCGGGACACACAGAAATATAAACCTTTCAAGAGTCAAGTAAAGAGTGTAAGGCCGTCTCTGAGACTACTTTCA
GAGAAGATCCTTGGGCTCCAGGTCCAGCAGGCGGAGCACTGTTCAATTCAGGATGCCCAGGCAACAATGAGGCTGTACGT
CATGGTGAAGCAGTGGGAGAGCATGGCCCGAGATAGTCGCCCCCTGCTGACCGCTCCGGACCACTGCAGTGACGACGCC

Alignment

ORF - retro_nleu_2930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.51 %
• Parental protein coverage: 88.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PASGPGAVVRPPKAPEDFSQNWKALQEWLLKQKSQAPEKPLVISQMGSKKKPKIMQRNKKETSPQVKGEE
          P.SGPGAVVRPPKAPEDFSQN.KALQEWLLKQKSQA.EKPLVISQMGSKKKPKI.Q.NKKETSPQVKGEE
Retrocopy PGSGPGAVVRPPKAPEDFSQN*KALQEWLLKQKSQASEKPLVISQMGSKKKPKIIQQNKKETSPQVKGEE

Parental  MPAGKDQEASRGSVPSGSRMDRKVPAPRTKASGAEHNKKGTKERTNGDVVPERGDIKHKKRKAKEAAPAL
          MPAGKDQEA.RGSVPS.S.MDRK.P.PRTKASGAEHNKKGTKERTNGD.VPERGDIKHKKRKAKEA.PA.
Retrocopy MPAGKDQEAIRGSVPSSSKMDRKAPVPRTKASGAEHNKKGTKERTNGDIVPERGDIKHKKRKAKEAVPAP

Parental  PTEEDIWFDDVDPADIEAAIGPEAAKIARKQLGQSEGSVSLSLMKEQAFGGLTRALALDCEMVGVGPKGE
          PTEEDIWFDDVDPADIEAAIGPEAAK.ARKQ.GQSEGSVSLSLMK.QAFGGLTRALALDCEMVGVGPKGE
Retrocopy PTEEDIWFDDVDPADIEAAIGPEAAKTARKQVGQSEGSVSLSLMKTQAFGGLTRALALDCEMVGVGPKGE

Parental  ESVAARVSIVNQYGKCVYDKYVKPAEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEILKGRILVGHAL
          ESVAARVSI.NQYGKCVYDKYVKP.EPVTDYRTAVSGI.P.NLKQGEELEVVQKEV.E.LKGRILVGHAL
Retrocopy ESVAARVSIMNQYGKCVYDKYVKPTEPVTDYRTAVSGIQPKNLKQGEELEVVQKEVVETLKGRILVGHAL

Parental  HNDLKVLFLDHPKKKIRDTQKYKPFKSQVKSGRPSLRLLSEKILGLQVQQAEHCSIQDAQAAMRLYVMVK
          HNDLKVLFLDHPKKKIRDTQKYKPFKSQVKS.RPSLRLLSEKILGLQVQQAEHCSIQDAQA.MRLYVMV.
Retrocopy HNDLKVLFLDHPKKKIRDTQKYKPFKSQVKSVRPSLRLLSEKILGLQVQQAEHCSIQDAQATMRLYVMV-

Parental  KEWESMARYRRPLLTAPDHCSDDA
          K.WESMAR..RPLLTAPDHCSDDA
Retrocopy KQWESMARDSRPLLTAPDHCSDDA

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_2930 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000012817	1 retrocopy	retro_mdom_1839,
Mus musculus	ENSMUSG00000052406	2 retrocopies	retro_mmus_1006, retro_mmus_2104,
Nomascus leucogenys	ENSNLEG00000012742	1 retrocopy	retro_nleu_3048,
Nomascus leucogenys	ENSNLEG00000013130	1 retrocopy	retro_nleu_2930 ,
Pongo abelii	ENSPPYG00000019735	1 retrocopy	retro_pabe_1278,