RetrogeneDB ID: retro_nleu_642

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397269.1:21412977..21413574(+)
• Located in intron of: ENSNLEG00000004433

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC13
• Ensembl ID: ENSNLEG00000004482
• Aliases: None
• Description: None

Sequence

>retro_nleu_642
ATGGTGTCAGTAATTAACACTGTGGATACCTCCCATAAGGATATGATTCATGATGCCCAGATGGACTACTATGGCACCCG
CCTGGCAACCTGCTCATCAGAAAAATCTGTCAAAATCTTCAAAGTGCACAACAGAGGGCAGATCCTCATTGCCAGCCTCA
GAAGTCATGATAGTCCTATGTGGCAAGTGGCCTGGGCTCACCCCACATATGGCAATATCCTGGCATTGTGCTCCTATGAT
TGGAAAGTCATTATCTGGAAAGAGGAAAACGGCACCTGGGAGAAGACCCACGACTCCTCAGGATATGACTCCTCGGTGAA
CTCTGTGTGCTAGGCCCCCCATGACTACGGCCTGATCCTGGCCTGTGGGAGCTCAGATGGGGCCATCTTCCTGTTGACTT
ATACAGGGGAAGGCCAATGGGAAGTGAAGATCAACAACGCTCACACCATTGGCTGCAATGCTGTCAGCTGGGCCCCTGCT
GTTGTACCTGGAAGCCTCATAGACCAGCTGTTCAGGCAGAAACCCAATTACGTCAAGAAGTTTGCATCAGGCGGCTGTGA
CAACCTCTTCAAGGATGGCCAGTGGAAGGAGGAGCAG

Alignment

ORF - retro_nleu_642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83. %
• Parental protein coverage: 53.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSVINTVDTSHEDMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQILIADLRGHEGPVWQVAWAHPMY
          MVSVINTVDTSH.DMIHDAQMDYYGTRLATCSS..SVKIF.V.N.GQILIA.LR.H..P.WQVAWAHP.Y
Retrocopy MVSVINTVDTSHKDMIHDAQMDYYGTRLATCSSEKSVKIFKVHNRGQILIASLRSHDSPMWQVAWAHPTY

Parental  GNVLASCSYDRKVIIWREENGTWEKSHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQW
          GN.LA.CSYD.KVIIW.EENGTWEK.H...G.DSSVNSVC.APHDYGLILACGSSDGAI.LLTYTGEGQW
Retrocopy GNILALCSYDWKVIIWKEENGTWEKTHDSSGYDSSVNSVC*APHDYGLILACGSSDGAIFLLTYTGEGQW

Parental  EVKKINNAHTIGCNAVSWAPAVVPGSLIDQPSGQKPNYIKRFASGGCDNLIK--LWKEEE
          EV.KINNAHTIGCNAVSWAPAVVPGSLIDQ...QKPNY.K.FASGGCDNL.K...WKEE.
Retrocopy EV-KINNAHTIGCNAVSWAPAVVPGSLIDQLFRQKPNYVKKFASGGCDNLFKDGQWKEEQ

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_642 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574, retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159, retro_mmus_3443,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642 ,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917,