RetrogeneDB ID: retro_pabe_184

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:40578282..40578675(+)
• Located in intron of: ENSPPYG00000005304

Retrocopy information

• Ensembl ID: ENSPPYG00000005305
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSPPYG00000002304
• Aliases: None
• Description: 40S ribosomal protein S24 [Source:UniProtKB/Swiss-Prot;Acc:Q5RAQ8]

Sequence

>retro_pabe_184
ATGAACGACACCGTAACTATCCGCACTAGAAAGTTCATGACCAACCGACTACTTCAGAGGAAACAAATGGTCATTGATGT
CCTTCACCCCGGGAAGGCAACAGTGCCTAAGACAGAAATTCGGGAAAAACTAGCCAAAATGTACAAGACCACACCGGATG
TCATCTTTGTATTTGGATTCAGAACTCATTTTGGTGGTGGCAAGACAACTGGCTTTGGCATGATTTATGATTCCCTGGAT
TATGCAAAGAAAAATGAACCCAAACATAGACTTGCAAGACATGGCCTGTATGAGAAGAAAAAGACCTCAAGAAAGCAACG
AAAGGAACGCAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGTGA

Alignment

ORF - retro_pabe_184 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTT
          MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTT
Retrocopy MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTT

Parental  GFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKK
          GFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKK
Retrocopy GFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKK

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	0.11 RPM	4.09 RPM
SRP007412_cerebellum	0.00 RPM	7.66 RPM
SRP007412_heart	0.21 RPM	7.86 RPM
SRP007412_kidney	0.30 RPM	8.22 RPM
SRP007412_liver	0.12 RPM	3.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_184 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_184 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000000189	4 retrocopies	retro_dord_248, retro_dord_498, retro_dord_717, retro_dord_766,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Monodelphis domestica	ENSMODG00000025091	3 retrocopies	retro_mdom_1303, retro_mdom_1706, retro_mdom_1914,
Mus musculus	ENSMUSG00000025290	13 retrocopies	retro_mmus_1101, retro_mmus_1462, retro_mmus_1589, retro_mmus_1592, retro_mmus_1599, retro_mmus_2134, retro_mmus_2332, retro_mmus_2497, retro_mmus_2984, retro_mmus_3162, retro_mmus_321, retro_mmus_3233, retro_mmus_602,
Ornithorhynchus anatinus	ENSOANG00000006329	1 retrocopy	retro_oana_54,
Pongo abelii	ENSPPYG00000002304	1 retrocopy	retro_pabe_184 ,
Sarcophilus harrisii	ENSSHAG00000008090	3 retrocopies	retro_shar_276, retro_shar_303, retro_shar_697,
Sus scrofa	ENSSSCG00000010328	8 retrocopies	retro_sscr_1212, retro_sscr_14, retro_sscr_242, retro_sscr_289, retro_sscr_491, retro_sscr_564, retro_sscr_718, retro_sscr_902,
Tarsius syrichta	ENSTSYG00000006715	1 retrocopy	retro_tsyr_1919,
Tursiops truncatus	ENSTTRG00000007845	3 retrocopies	retro_ttru_1462, retro_ttru_740, retro_ttru_86,