RetrogeneDB ID: retro_nleu_1966

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397319.1:12638668..12639218(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000001496
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PEBP1
• Ensembl ID: ENSNLEG00000000322
• Aliases: None
• Description: None

Sequence

>retro_nleu_1966
ATGCCGGTGGACCTCAGCAAGTGGTCCGGGCCCTTGAGCCTGCAAGAAATGGACGAGCAGCCACAGCACCTGCTGCATGT
CACCTACGCCCAGGCGGCGGTGGACGAGCTGGGCAAAGTGCTGACGCCCACCCAGGTTAGGAATAGACCCACCAGCATTT
CGTGGGATGGTCTTGATTCAGGGAAGCTCTACACCTTGGTCCTGACAGACCCGGATGCTCCCAGCAGGAAGGATCCCAAA
TACAGAGAATGGCATCATTTCCTGGTGGTCAACATGAAGGGCAATGACATCAGCAGTGGCACAGTCCTCTCCGATTATGT
GGGCTCGGGGCCTCCCCAAGGGCACAGGTCTCCACCGCTATGTCTGGCTGGTTTATGAGCAGGACAGGCCACTAAAGTGT
GACGAGCCCATCCTCAGCAACCGATCTGGAGACCAGAAGGTGGCGTCCTTCCGTAAAAAGTACGAGCTCGGGGCCCTGGT
GGCCGGCACCTGTTAACAGGCTGAGTGGGACGACTATGTGCCCAAACTGTACAAGCAGTTGTCTGGGAAG

Alignment

ORF - retro_nleu_1966 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPVDLSKWSGPLSLQEVDEQPQHPLHVTYAGAAVDELGKVLTPTQVHRTAGPPGWDPAETGPGAVGRFSL
          MPVDLSKWSGPLSLQE.DEQPQH.LHVTYA.AAVDELGKVLTPTQV........WD......G......L
Retrocopy MPVDLSKWSGPLSLQEMDEQPQHLLHVTYAQAAVDELGKVLTPTQVRNRPTSISWDGLDS--GKLYTLVL

Parental  RVSRPPRPEVPGSIEWHHFLVVNMKGNDISSGTVLSDYVGSGP-PKGTGLHRYVWLVYEQDRPLKCDEPI
          .....P....P...EWHHFLVVNMKGNDISSGTVLSDYVGSGP.PKGTGLHRYVWLVYEQDRPLKCDEPI
Retrocopy TDPDAPSRKDPKYREWHHFLVVNMKGNDISSGTVLSDYVGSGP>PKGTGLHRYVWLVYEQDRPLKCDEPI

Parental  LSNRSGDHRGKFKVASFRKKYELRAPVAGTCYQAEWDDYVPKLYEQLSGK
          LSNRSGD......VASFRKKYEL.A.VAGTC.QAEWDDYVPKLY.QLSGK
Retrocopy LSNRSGDQK----VASFRKKYELGALVAGTC*QAEWDDYVPKLYKQLSGK

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_1966 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 17 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016143	2 retrocopies	retro_amel_1355, retro_amel_754,
Bos taurus	ENSBTAG00000018115	2 retrocopies	retro_btau_1183, retro_btau_705,
Canis familiaris	ENSCAFG00000009910	1 retrocopy	retro_cfam_526,
Callithrix jacchus	ENSCJAG00000009314	2 retrocopies	retro_cjac_1410, retro_cjac_818,
Erinaceus europaeus	ENSEEUG00000003689	1 retrocopy	retro_eeur_292,
Felis catus	ENSFCAG00000002277	3 retrocopies	retro_fcat_1317, retro_fcat_1360, retro_fcat_299,
Myotis lucifugus	ENSMLUG00000002259	7 retrocopies	retro_mluc_103, retro_mluc_1612, retro_mluc_1742, retro_mluc_2357, retro_mluc_2373, retro_mluc_984, retro_mluc_998,
Macaca mulatta	ENSMMUG00000005098	4 retrocopies	retro_mmul_1621, retro_mmul_2272, retro_mmul_328, retro_mmul_442,
Mustela putorius furo	ENSMPUG00000002861	3 retrocopies	retro_mputfur_1228, retro_mputfur_1361, retro_mputfur_223,
Mus musculus	ENSMUSG00000032959	4 retrocopies	retro_mmus_138, retro_mmus_1857, retro_mmus_2314, retro_mmus_542,
Nomascus leucogenys	ENSNLEG00000000322	1 retrocopy	retro_nleu_1966 ,
Oryctolagus cuniculus	ENSOCUG00000008395	2 retrocopies	retro_ocun_1329, retro_ocun_1900,
Otolemur garnettii	ENSOGAG00000001740	1 retrocopy	retro_ogar_2750,
Rattus norvegicus	ENSRNOG00000001136	3 retrocopies	retro_rnor_1223, retro_rnor_46, retro_rnor_541,
Ictidomys tridecemlineatus	ENSSTOG00000004085	2 retrocopies	retro_itri_1603, retro_itri_961,
Tupaia belangeri	ENSTBEG00000000177	2 retrocopies	retro_tbel_272, retro_tbel_2728,
Tursiops truncatus	ENSTTRG00000000658	1 retrocopy	retro_ttru_1164,