RetrogeneDB ID: retro_nleu_647

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397269.1:29053295..29054160(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000005725
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STOM
• Ensembl ID: ENSNLEG00000017145
• Aliases: None
• Description: None

Sequence

>retro_nleu_647
ATGGCCGAGAAGCGGCACACACTGGACTCCGAAGCCCAGCGGCTCCCCAACTCCTTCAAGGACAGCCCCAGTAAGGGCCT
TGGACCTTGCGGATGGATTTTGGTGGCGTTCTCATTCTTATTAACAGTTATAACTTTCCCAGTCTCAATATGGATGTGCA
TAAAGATTATAAAAGAGTATGAAAGAGCCATCATCTTTAGATTGGGTCGCATTTTACAAGGAGGAGCCAAAGGACCTGGT
TTGTTTTTTATTCTGCCATGCACTGACAGCTTCATCAAAGTGGACATGAGAACAATTTCATTTGATATTCCTCCTCAGGA
GATCCTCACAAAGGATTCAGTGACAATTAGCGTGGATGGTGTGGTCTATTAACCGTGTTCAGAATGCAACCCTGGCTGTG
GCAAATATCACCAATGCTGACTCGGTGACCCGTCTTTTGGCACAAACTACTCTGAGGAATGTTCTGGGCAACAAGAACCT
TTCTCAGATCCTCTCTGACAGAGAAGAAATTGCACACAACATGCAGTCTACTCTGGATGATGCCACTGATGCCTGGGGAA
TAAAGGTGGAGCGTGTGGAAATTAAGGATGTGAAACTACCTGTGCAGCTCCAGAGAGCTATGGCTGCAGAAGCAGAAGCG
TCCCGCGAGGCCCGCGCCAAGGTTATTGCAGCCAAAGGAGAAATGAATGCATCCAGGGCTCTGAAAGAAGCCTCCATGGT
CATCACTGAATCTCCTGCAGCCCTTCAGCTCTGGTACCTGCAGACACTGACCACCATTGCTGCTGAGAAAAACTCAACAA
TTGTCTTCCCTCTGCCCATAGATATGCTGCAAGGAATCATAGGGGCAAAACACAGCCATCTAGGC

Alignment

ORF - retro_nleu_647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEKRHTLDSEAQRLPDSFKDSPSKGLGPCGWILVAFSFLFTVITFPISIWMCIKIIKEYERAIIFRLGR
          MAEKRHTLDSEAQRLP.SFKDSPSKGLGPCGWILVAFSFL.TVITFP.SIWMCIKIIKEYERAIIFRLGR
Retrocopy MAEKRHTLDSEAQRLPNSFKDSPSKGLGPCGWILVAFSFLLTVITFPVSIWMCIKIIKEYERAIIFRLGR

Parental  ILQGGAKGPGLFFILPCTDSFIKVDMRTISFDIPPQEILTKDSVTISVDGVVY-YRVQNATLAVANITNA
          ILQGGAKGPGLFFILPCTDSFIKVDMRTISFDIPPQEILTKDSVTISVDGVVY..RVQNATLAVANITNA
Retrocopy ILQGGAKGPGLFFILPCTDSFIKVDMRTISFDIPPQEILTKDSVTISVDGVVY>NRVQNATLAVANITNA

Parental  DSATRLLAQTTLRNVLGTKNLSQILSDREEIAHNMQSTLDDATDAWGIKVERVEIKDVKLPVQLQRAMAA
          DS.TRLLAQTTLRNVLG.KNLSQILSDREEIAHNMQSTLDDATDAWGIKVERVEIKDVKLPVQLQRAMAA
Retrocopy DSVTRLLAQTTLRNVLGNKNLSQILSDREEIAHNMQSTLDDATDAWGIKVERVEIKDVKLPVQLQRAMAA

Parental  EAEASREARAKVIAAEGEMNASRALKEASIVITESPAALQLRYLQTLTTIAAEKNSTIVFPLPIDMLQGI
          EAEASREARAKVIAA.GEMNASRALKEAS.VITESPAALQL.YLQTLTTIAAEKNSTIVFPLPIDMLQGI
Retrocopy EAEASREARAKVIAAKGEMNASRALKEASMVITESPAALQLWYLQTLTTIAAEKNSTIVFPLPIDMLQGI

Parental  IGAKHSHLG
          IGAKHSHLG
Retrocopy IGAKHSHLG

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_647 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015723	1 retrocopy	retro_dnov_2496,
Nomascus leucogenys	ENSNLEG00000017145	1 retrocopy	retro_nleu_647 ,
Otolemur garnettii	ENSOGAG00000002879	2 retrocopies	retro_ogar_2886, retro_ogar_291,
Oreochromis niloticus	ENSONIG00000013021	1 retrocopy	retro_onil_33,