RetrogeneDB ID: retro_pabe_2222

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:68769894..68770249(+)
• Located in intron of: ENSPPYG00000013706

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRB3
• Ensembl ID: ENSPPYG00000009457
• Aliases: None
• Description: crumbs homolog 3 (Drosophila) [Source:HGNC Symbol;Acc:20237]

Sequence

>retro_pabe_2222
GGCCTGGGGCTGCTCCTGGCGCTGGGCCTGCCGCTGCTGTCGTCCCCGGGAACGACCCTGGGCGCAAATATCAACCCCTT
CTGCAAATGAGAGTAGCATTGTTTTGCCTACACCCACCAGCTCCGGCTCCAATGGAGCCCTGTTTCGGGGGGCCGTCACT
GCTATCATCTTGGTCCTCTGATTCCTGGCCGTCTTGTTCCTGGCAGTGGGGCTGGCACTATTGGTGCGGAAGCTTTGGGA
GATGCGGCAGACGGAGGGCACCTACTGGCCCAGCAGCAAGGAGCAGTTCTCCTATGTGGCTGAGGCCTGGGCCCCTCAGT
ACTCCAATGAGACCTTGTGGGGCTGCCTGCACATC

Alignment

ORF - retro_pabe_2222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 96.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLGLLLALGLPFLLARWG-RAWGQIRTASTNENSTVLPSSTSSSSDSNLPQGAITAIIVVFSILAALLLA
          GLGLLLALGLP.LL...G.R.W.QI.T.S.NE.S.VLP..TSS.S...L..GA.TAII.V...LA.L.LA
Retrocopy GLGLLLALGLP-LLSSPG>RPWAQISTPSANESSIVLPTPTSSGSNGALFRGAVTAIILVL*FLAVLFLA

Parental  VGLALLVWKLREKRQTEGTYRPSSEEQFSHAAEARAPQDSKETVRGCLPI
          VGLALLV.KL.E.RQTEGTY.PSS.EQFS..AEA.APQ.S.ET..GCL.I
Retrocopy VGLALLVRKLWEMRQTEGTYWPSSKEQFSYVAEAWAPQYSNETLWGCLHI

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	0.00 RPM	0.11 RPM
SRP007412_cerebellum	0.49 RPM	0.12 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	2.15 RPM
SRP007412_liver	0.00 RPM	2.14 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2222 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2222 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2747
Gorilla gorilla	retro_ggor_1910
Macaca mulatta	retro_mmul_1434

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016567	1 retrocopy	retro_cjac_868,
Homo sapiens	ENSG00000130545	2 retrocopies	retro_hsap_2747, retro_hsap_3478,
Gorilla gorilla	ENSGGOG00000007070	2 retrocopies	retro_ggor_1910, retro_ggor_2345,
Macaca mulatta	ENSMMUG00000005599	1 retrocopy	retro_mmul_1434,
Nomascus leucogenys	ENSNLEG00000015936	1 retrocopy	retro_nleu_1543,
Pongo abelii	ENSPPYG00000009457	2 retrocopies	retro_pabe_2222 , retro_pabe_2873,
Pan troglodytes	ENSPTRG00000010367	1 retrocopy	retro_ptro_2984,
Rattus norvegicus	ENSRNOG00000047322	1 retrocopy	retro_rnor_1506,
Ictidomys tridecemlineatus	ENSSTOG00000002396	1 retrocopy	retro_itri_781,