RetrogeneDB ID: retro_nleu_1689

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397304.1:4656875..4657735(-)
• Located in intron of: ENSNLEG00000001067

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSNLEG00000004191
• Aliases: None
• Description: None

Sequence

>retro_nleu_1689
ATGGCCAACTTCAATGATCGTGTGTTGGCTGAGGAGAAGGTATGCAGAGCTGCTAAATTCATCACTCATGCACCCCCAGG
AGAATTTAATGAAGTATTCAGTGATATTCGGCTACTACATAATAATGACAGTCTCCTCAGGGAAAGGGCAGCACATGCAT
TTGCTCATTATAATATGGATCAGTTCACACCTGTGAAGATGGAAGGATATGAAGATCAGGTCTTTAATTACAGAGCATGG
TGACCTGGGTAATAGCAGAGTTTTAGATCCGAGAAACAAAATTTCCTTTACATTTAATCACTTATAGAGATAAGCAAGTG
ACCCCCAGCCAGAACAAGTAGATGGAGGTCTCAAGTCTTGGAGAGAATCCCGTGACAGTGCTTTAAGAGCCTATGTGAAA
GACCATTATTCCAACGGCTTCTGTACTGTTTATGCTAAAACTATCGATGGGCCACAGACTATTATTGCATGTATTGAAAG
CCATGAGTGTCAGCCTAAAAACTTCTGGAATGGTCGTTGGAGATCAGAGTGGAAGTTTACCATCACACCACCTACAGCCC
AGGTGGTTGGAGTGCTTAAGATTCAGGTTCACTATTATGAAGATGGCAGTGTTCAGTTGGTTAGTCATAAAGATGTACAG
GATTCACTAACTGTTTCGAATGACGGACAAACTGCCAAGGAGTTTATTAAAATCATAGAGAATGCAGAAAATGAATATCA
GACAGCAGTTAGTGAAAACTGTCAAACAATGTCAGATACCACATTCAAGGTCTTGCACTGGCAGCTTCCGGTTACCCGCA
CCAAAATTGACCGGAACAAGATTACTCAGCTACAACATTGGCAAAGAAATGCAGAATGCC

Alignment

ORF - retro_nleu_1689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADFDDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLRKGAAHAFAQYNMDQFTPVKIEGY
          MA.F.DRV..EEKV..AAKFITHAPPGEFNEVF.D.RLL.NND.LLR..AAHAFA.YNMDQFTPVK.EGY
Retrocopy MANFNDRVLAEEKVCRAAKFITHAPPGEFNEVFSDIRLLHNNDSLLRERAAHAFAHYNMDQFTPVKMEGY

Parental  EDQV-LITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGGLKSWRESCDSALRAYVKDHYSNG
          EDQV.LITEHGDLGNSR.LDPRNKISF.F.HL...ASDPQPE.VDGGLKSWRES.DSALRAYVKDHYSNG
Retrocopy EDQV>LITEHGDLGNSRVLDPRNKISFTFNHL*R*ASDPQPEQVDGGLKSWRESRDSALRAYVKDHYSNG

Parental  FCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSH
          FCTVYAKTIDG.QTIIACIESH..QPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDG.VQLVSH
Retrocopy FCTVYAKTIDGPQTIIACIESHECQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGSVQLVSH

Parental  KDVQDSLTVSNEAQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKI-LSYK
          KDVQDSLTVSN..QTAKEFIKIIENAENEYQTA.SEN.QTMSDTTFK.L..QLPVTRTKID.NKI.LSY.
Retrocopy KDVQDSLTVSNDGQTAKEFIKIIENAENEYQTAVSENCQTMSDTTFKVLHWQLPVTRTKIDRNKI>LSYN

Parental  IGKEMQNA
          IGKEMQNA
Retrocopy IGKEMQNA

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_1689 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	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Callithrix jacchus	ENSCJAG00000013548	3 retrocopies	retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus	ENSCPOG00000014532	1 retrocopy	retro_cpor_1155,
Dipodomys ordii	ENSDORG00000000671	3 retrocopies	retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus	ENSFCAG00000013303	2 retrocopies	retro_fcat_700, retro_fcat_746,
Homo sapiens	ENSG00000116489	2 retrocopies	retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla	ENSGGOG00000023677	1 retrocopy	retro_ggor_1216,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Macaca mulatta	ENSMMUG00000015668	2 retrocopies	retro_mmul_2612, retro_mmul_942,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys	ENSNLEG00000004191	1 retrocopy	retro_nleu_1689 ,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Otolemur garnettii	ENSOGAG00000014074	4 retrocopies	retro_ogar_1640, retro_ogar_2159, retro_ogar_3217, retro_ogar_845,
Pongo abelii	ENSPPYG00000001021	2 retrocopies	retro_pabe_2116, retro_pabe_3789,
Pan troglodytes	ENSPTRG00000001110	2 retrocopies	retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Tupaia belangeri	ENSTBEG00000001727	5 retrocopies	retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,