RetrogeneDB ID: retro_nleu_53

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397264.1:48482782..48483526(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018183
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SPIC
• Ensembl ID: ENSNLEG00000006232
• Aliases: None
• Description: Spi-C transcription factor (Spi-1/PU.1 related) [Source:HGNC Symbol;Acc:29549]

Sequence

>retro_nleu_53
ATGACATGTGTTGAACAAGACAAGCTGGGTCAAGCATTTGAGGATGCTTTTGAGGTTCTGAGGCAACATTCAACTGGAGA
TCTTCAGTACTTGCCAGATTACAAAAATTACCTGGCTTTAATCAACCATCATCCTCATGTCAAAGGAAATTCCAGCTGCT
ATGGAGTGTTGCCTACAGAGGAGCCTGTCTATAATTGGAGAACGGTAATTAACAGTGCTGTGGACTTCTATTTTGAAGGA
AATATTCATCAATCTCTGCAGAACATAACTGAAAACCAGCTGGTACAACCCACTGTTCTCCAGCAAAAGGGGGGAAAAGG
CAGGAAGAAGCTCCGACTGTTTGAATACCTTCACAAATCCCTGTGTAATCCAGAGATGGTATCTTGTTTTCAGTGGGTAG
ATATAACCAAAGGCATCTTTCAGTTTGTATCAAAAAACAAAGACAAACTTGCCGAGCTCTGGGGGAAAACAAAAGGCAAC
AGGAAGACCATGACTTACCAGAAAATGGCCAGGGCACTGAGAAATTACAGAAGAAGTGGGGAAATTACCAAAATCTGGAG
GAAGCTGACTTACCATTTCAGTGAGGCCATTCTCCAAAGACTCTCTCCATCCTATTTCCTGGGGAAAGACATCTACTACT
CACAATGTGTTCAACCTGATCAAGAATATCTCAGTTTAAATAACTGGAATGCAAATTATACTTATACATATGCCAATTAC
CATGCGCTAAATCACCATGATTGC

Alignment

ORF - retro_nleu_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TCVEQDKLGQAFEDAFEVLRQHSTGDLQYSPDYRNYLALINHRPHVKGNSSCYGVLPTEEPVYNWRTVIV
          TCVEQDKLGQAFEDAFEVLRQHSTGDLQY.PDY.NYLALINH.PHVKGNSSCYGVLPTEEPVYNWRTVI.
Retrocopy TCVEQDKLGQAFEDAFEVLRQHSTGDLQYLPDYKNYLALINHHPHVKGNSSCYGVLPTEEPVYNWRTVIN

Parental  SIRPSLSWGSVARSRLTATSASQVQAILLPQPPNHGRKKLRLFEYLHESLYNPEMASCIQWVDKTKGIFQ
          S.......G....S....T....VQ...L.Q....GRKKLRLFEYLH.SL.NPEM.SC.QWVD.TKGIFQ
Retrocopy SAVDFYFEGNIHQSLQNITENQLVQPTVLQQKGGKGRKKLRLFEYLHKSLCNPEMVSCFQWVDITKGIFQ

Parental  FVSKNKEKLAELWGKRKGNRKTMTYQKMARALRNYGRSGEITKIRRKLTYQFSEAILQRLSPSYFLGKEI
          FVSKNK.KLAELWGK.KGNRKTMTYQKMARALRNY.RSGEITKI.RKLTY.FSEAILQRLSPSYFLGK.I
Retrocopy FVSKNKDKLAELWGKTKGNRKTMTYQKMARALRNYRRSGEITKIWRKLTYHFSEAILQRLSPSYFLGKDI

Parental  FYSQCVQPDQEYLSLNNWNANYNYTYANYHELNHHDC
          .YSQCVQPDQEYLSLNNWNANY.YTYANYH.LNHHDC
Retrocopy YYSQCVQPDQEYLSLNNWNANYTYTYANYHALNHHDC

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_53 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009904	2 retrocopies	retro_btau_1281, retro_btau_1837,
Callithrix jacchus	ENSCJAG00000001906	1 retrocopy	retro_cjac_3835,
Dasypus novemcinctus	ENSDNOG00000004496	1 retrocopy	retro_dnov_759,
Equus caballus	ENSECAG00000009614	1 retrocopy	retro_ecab_542,
Echinops telfairi	ENSETEG00000004217	6 retrocopies	retro_etel_1675, retro_etel_2007, retro_etel_2008, retro_etel_593, retro_etel_929, retro_etel_933,
Loxodonta africana	ENSLAFG00000015661	1 retrocopy	retro_lafr_912,
Myotis lucifugus	ENSMLUG00000011052	1 retrocopy	retro_mluc_2169,
Macaca mulatta	ENSMMUG00000020873	1 retrocopy	retro_mmul_1245,
Nomascus leucogenys	ENSNLEG00000006232	1 retrocopy	retro_nleu_53 ,
Oryctolagus cuniculus	ENSOCUG00000008070	1 retrocopy	retro_ocun_161,
Otolemur garnettii	ENSOGAG00000015148	1 retrocopy	retro_ogar_1782,
Rattus norvegicus	ENSRNOG00000005720	1 retrocopy	retro_rnor_1519,
Ictidomys tridecemlineatus	ENSSTOG00000015457	3 retrocopies	retro_itri_1785, retro_itri_235, retro_itri_29,
Tursiops truncatus	ENSTTRG00000017205	1 retrocopy	retro_ttru_1708,