RetrogeneDB ID: retro_pabe_1990

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:40896964..40897298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRNP27
• Ensembl ID: ENSPPYG00000012332
• Aliases: None
• Description: small nuclear ribonucleoprotein 27kDa (U4/U6.U5) [Source:HGNC Symbol;Acc:30240]

Sequence

>retro_pabe_1990
CGCTCGCGATCCCGCACTAGACGCTCCCGATCTCAGACGACAAAATCCACACTCGTCCCTCTCAACGAATGAAGAGAGAT
GAGAAAAGAAAGAAACAAAGAGCAAAGAATGGCAGATTACTGAGGAAGACTTAGAGGGCAAAACAGAGGAAGAAATAGAA
ATGATGAAGTTAATGGAATTTGCCTCCTTTGACTCCACAAAAGGTAAGAAGGTGGATTGCTCTGTAAATGCCTATGCCAT
AAATGTCTCTCAGAAGAGGAAGTACAGGCAGTACATGAATCGAAAAGGTGGATTCCACAGACCTTTGGATTTCATTGCAT
GAGAATTGAAATGT

Alignment

ORF - retro_pabe_1990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.75 %
• Parental protein coverage: 69.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSRSPRRHRSTSPSPSRLKERRD-EEKKETKETKSKERQITEEDLEGKTEEEIEMMKLMGFASFDSTKGK
          RSRS..R........S.L......EE..E.KETKSKE.QITEEDLEGKTEEEIEMMKLM.FASFDSTKGK
Retrocopy RSRSRTRRSRSQTTKSTLVPLNE>EER*EKKETKSKEWQITEEDLEGKTEEEIEMMKLMEFASFDSTKGK

Parental  KVDGSVNAYAINVSQKRKYRQYMNRK-WIQQTFGFHCMRLKC
          KVD.SVNAYAINVSQKRKYRQYMNRK........F....LKC
Retrocopy KVDCSVNAYAINVSQKRKYRQYMNRKGGFHRPLDFIA*ELKC

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	5.42 RPM
SRP007412_cerebellum	0.00 RPM	8.15 RPM
SRP007412_heart	0.03 RPM	5.63 RPM
SRP007412_kidney	0.03 RPM	5.70 RPM
SRP007412_liver	0.00 RPM	5.45 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1990 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1990 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000037746	4 retrocopies	retro_btau_1352, retro_btau_375, retro_btau_514, retro_btau_515,
Choloepus hoffmanni	ENSCHOG00000003042	1 retrocopy	retro_chof_2589,
Echinops telfairi	ENSETEG00000017344	1 retrocopy	retro_etel_655,
Homo sapiens	ENSG00000124380	1 retrocopy	retro_hsap_3387,
Mus musculus	ENSMUSG00000001158	2 retrocopies	retro_mmus_1977, retro_mmus_2105,
Oryctolagus cuniculus	ENSOCUG00000022967	1 retrocopy	retro_ocun_1281,
Pongo abelii	ENSPPYG00000012332	2 retrocopies	retro_pabe_1990 , retro_pabe_2782,
Pan troglodytes	ENSPTRG00000012022	1 retrocopy	retro_ptro_2300,
Sus scrofa	ENSSSCG00000025674	1 retrocopy	retro_sscr_285,