RetrogeneDB ID: retro_pabe_2097

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:4054639..4055263(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB6A
• Ensembl ID: ENSPPYG00000003663
• Aliases: None
• Description: Ras-related protein Rab-6A [Source:UniProtKB/Swiss-Prot;Acc:Q5RAV6]

Sequence

>retro_pabe_2097
ATGTCCACGGGCGGAGACTAGGGGAATCCGCTGAGGAAATTCAAGCTGGAGTTCCTGGGGGAGCAAAGCGTTGCAAAGAC
GTCTTTGATCACCAGATTCATGTATGACAGTTTTGACAACACCTATCAGGCAACAATTGGCATTGACTTTTTATCAAAAA
CTATGTACTTGGAGGATGGAACAATCAGGCTTCGGCTGTGGGATACTGCGGGTCAGGAACGTCTCCGTAGCCTTATTCCC
AGTTACAGCCGTGATTCTGCTGCAGCTGTAGCAGTTTACGATATCACAAATGTTAACTCCTTCCAGCAAACTACAAAGTG
GATTGATGATGTCAGAACAGAAAGAGGAAGTGATGTTATCATCACGCTAGTAGGAAATAAAACAGATCTTGCTGACAAGA
GGCAAGTGTCAATTGAGGACGGAGAGAGGAAAGCCAAAGAGCTGAATGTTATGTTTATTGAAACTAGGGCAAAAGCTGGA
TACAATGTAAAGCAGCTCTTTCGACGTGTAGCAGCAGTTTTGCCGGGAATGGAAAGCACACAGGACAGAAGCAGAGAAGA
CATGAGTGACATAAAACTGGAAAAGCCTCAGGAGCAACCAGTCAGCGAAGGAGGCTGTTCCTGC

Alignment

ORF - retro_pabe_2097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTGGDFGNPLRKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTA
          MSTGGD.GNPLRKFKL.FLGEQSV.KTSLITRFMYDSFDNTYQATIGIDFLSKTMYLED.T.RL.LWDTA
Retrocopy MSTGGD*GNPLRKFKLEFLGEQSVAKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDGTIRLRLWDTA

Parental  GQERFRSLIPSYIRDSTVAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIEE
          GQER.RSLIPSY.RDS..AV.VYDITNVNSFQQTTKWIDDVRTERGSDVII.LVGNKTDLADKRQVSIE.
Retrocopy GQERLRSLIPSYSRDSAAAVAVYDITNVNSFQQTTKWIDDVRTERGSDVIITLVGNKTDLADKRQVSIED

Parental  GERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGMESTQDRSREDMIDIKLEKPQEQPVSEGGCSC
          GERKAKELNVMFIET.AKAGYNVKQLFRRVAA.LPGMESTQDRSREDM.DIKLEKPQEQPVSEGGCSC
Retrocopy GERKAKELNVMFIETRAKAGYNVKQLFRRVAAVLPGMESTQDRSREDMSDIKLEKPQEQPVSEGGCSC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.06 RPM	213.03 RPM
SRP007412_cerebellum	0.00 RPM	129.63 RPM
SRP007412_heart	0.00 RPM	37.87 RPM
SRP007412_kidney	0.03 RPM	52.80 RPM
SRP007412_liver	0.00 RPM	32.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2097 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2097 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2097 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000992	1 retrocopy	retro_chof_859,
Echinops telfairi	ENSETEG00000009412	1 retrocopy	retro_etel_1486,
Homo sapiens	ENSG00000175582	1 retrocopy	retro_hsap_7,
Loxodonta africana	ENSLAFG00000009905	1 retrocopy	retro_lafr_430,
Mus musculus	ENSMUSG00000030704	1 retrocopy	retro_mmus_2400,
Nomascus leucogenys	ENSNLEG00000017098	1 retrocopy	retro_nleu_200,
Ornithorhynchus anatinus	ENSOANG00000031623	1 retrocopy	retro_oana_94,
Ochotona princeps	ENSOPRG00000001164	5 retrocopies	retro_opri_1098, retro_opri_20, retro_opri_606, retro_opri_797, retro_opri_993,
Ochotona princeps	ENSOPRG00000010355	6 retrocopies	retro_opri_1082, retro_opri_1085, retro_opri_1095, retro_opri_1118, retro_opri_247, retro_opri_858,
Pongo abelii	ENSPPYG00000003663	3 retrocopies	retro_pabe_2097 , retro_pabe_2191, retro_pabe_3537,
Ictidomys tridecemlineatus	ENSSTOG00000023497	3 retrocopies	retro_itri_1743, retro_itri_1827, retro_itri_1885,