RetrogeneDB ID: retro_pabe_513

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:36061335..36061527(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SS18L2
• Ensembl ID: ENSPPYG00000013979
• Aliases: None
• Description: synovial sarcoma translocation gene on chromosome 18-like 2 [Source:HGNC Symbol;Acc:15593]

Sequence

>retro_pabe_513
GACTGGCTGAGGGGCAAGGTGAAAGTCAATTAAGAGACTATCCAGCGGCTCCTTGAGGAGAATGACCAACTGATCTGCTG
TATTGTGGAGTATCAGAACAAGAGCCAGGCGAATGATTGTGTCCAGTGCCAGCTTGTGTTACATAGAAATCTCATTTATT
TGGCTACCATCGCAGATGCCAGCCCAACCAGT

Alignment

ORF - retro_pabe_513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.38 %
• Parental protein coverage: 83.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DWLRGKAEVNQETIQRLLEENDQLIRCIVEYQNKGRGNECVQYQHVLHRNLIYLATIADASPTS
          DWLRGK..VN.ETIQRLLEENDQLI.CIVEYQNK...N.CVQ.Q.VLHRNLIYLATIADASPTS
Retrocopy DWLRGKVKVN*ETIQRLLEENDQLICCIVEYQNKSQANDCVQCQLVLHRNLIYLATIADASPTS

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	12.66 RPM
SRP007412_cerebellum	0.00 RPM	15.93 RPM
SRP007412_heart	0.00 RPM	6.41 RPM
SRP007412_kidney	0.00 RPM	8.82 RPM
SRP007412_liver	0.00 RPM	13.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_513 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_513 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_557
Macaca mulatta	retro_mmul_2392

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000989	1 retrocopy	retro_acar_189,
Dipodomys ordii	ENSDORG00000015005	4 retrocopies	retro_dord_286, retro_dord_39, retro_dord_643, retro_dord_658,
Homo sapiens	ENSG00000008324	1 retrocopy	retro_hsap_557,
Loxodonta africana	ENSLAFG00000021542	2 retrocopies	retro_lafr_754, retro_lafr_92,
Myotis lucifugus	ENSMLUG00000013024	1 retrocopy	retro_mluc_21,
Macaca mulatta	ENSMMUG00000031677	1 retrocopy	retro_mmul_2392,
Nomascus leucogenys	ENSNLEG00000005848	1 retrocopy	retro_nleu_2639,
Ochotona princeps	ENSOPRG00000015198	4 retrocopies	retro_opri_401, retro_opri_516, retro_opri_542, retro_opri_593,
Pongo abelii	ENSPPYG00000013979	2 retrocopies	retro_pabe_513 , retro_pabe_651,