RetrogeneDB ID: retro_nleu_2956

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397521.1:232661..233162(-)
• Located in intron of: ENSNLEG00000026895

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSNLEG00000002137
• Aliases: None
• Description: None

Sequence

>retro_nleu_2956
ATGAACTGTCCAGCCCCTGTCGAGATCTCCTGTGACAACATGCGTTTTCTTGTAACTCACAACCCTACCAATGCTACTCT
CAACAAGTTCCCAGAGAAACTTAAGAAGTATGGAGTGACGACTTTGGTTCGAGTTTGTGATGCTACACATGATAAAGCTC
CAGTTGAAAAGGAAGGAATCCACATTCTAGATTGGCCATTTGATGATGGAGCTCCATCCCCTAATCAGATAGTAATTGAT
TGGTTAAACCTGTTATAAACCAAATTCCGTGAAGAGCCAGGTTGCTGTGTTGCAGTGCATTGTGTTGCGGGATTGGGAAG
GGCACCTGTGCTGGTTGCACTTGCTTTGATTGAATGTGGAATGAAGTACAAAGATGCAGTCCAGTTTATAAGACAAAAAA
GAAGGGGGGCATTTAATTCCAAACAGCTGCTTTACTTGGAGAAATACCGACCTAAGATGCGATTATGCTTCAGAGATACC
AATGGTCATTGCTGTGTTCAG

Alignment

ORF - retro_nleu_2956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDDG
          MN.PAPVEIS..NMRFL.THNPTNATLNKF.E.LKKYGVTTLVRVCDAT.DKAPVEKEGIH.LDWPFDDG
Retrocopy MNCPAPVEISCDNMRFLVTHNPTNATLNKFPEKLKKYGVTTLVRVCDATHDKAPVEKEGIHILDWPFDDG

Parental  APPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNS
          AP.PNQIV.DWLNLL.TKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKY.DAVQFIRQKRRGAFNS
Retrocopy APSPNQIVIDWLNLL*TKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYKDAVQFIRQKRRGAFNS

Parental  KQLLYLEKYRPKMRLRFRDTNGHCCVQ
          KQLLYLEKYRPKMRL.FRDTNGHCCVQ
Retrocopy KQLLYLEKYRPKMRLCFRDTNGHCCVQ

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_2956 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039121	1 retrocopy	retro_btau_638,
Callithrix jacchus	ENSCJAG00000006539	2 retrocopies	retro_cjac_3257, retro_cjac_566,
Homo sapiens	ENSG00000184007	4 retrocopies	retro_hsap_1069, retro_hsap_1754, retro_hsap_4331, retro_hsap_944,
Mus musculus	ENSMUSG00000028788	2 retrocopies	retro_mmus_1894, retro_mmus_2432,
Nomascus leucogenys	ENSNLEG00000000440	6 retrocopies	retro_nleu_1111, retro_nleu_1159, retro_nleu_1681, retro_nleu_169, retro_nleu_407, retro_nleu_893,
Nomascus leucogenys	ENSNLEG00000002137	3 retrocopies	retro_nleu_2880, retro_nleu_2956 , retro_nleu_3015,
Oryctolagus cuniculus	ENSOCUG00000002060	1 retrocopy	retro_ocun_1673,
Otolemur garnettii	ENSOGAG00000029603	1 retrocopy	retro_ogar_3341,
Pongo abelii	ENSPPYG00000001606	3 retrocopies	retro_pabe_1507, retro_pabe_808, retro_pabe_890,
Rattus norvegicus	ENSRNOG00000050044	1 retrocopy	retro_rnor_305,
Sus scrofa	ENSSSCG00000003605	1 retrocopy	retro_sscr_1186,
Ictidomys tridecemlineatus	ENSSTOG00000002775	2 retrocopies	retro_itri_1165, retro_itri_152,
Tupaia belangeri	ENSTBEG00000006790	1 retrocopy	retro_tbel_4601,
Tursiops truncatus	ENSTTRG00000016571	2 retrocopies	retro_ttru_1396, retro_ttru_1402,