RetrogeneDB ID: retro_pabe_2440

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:72468856..72469557(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSPPYG00000012825
• Aliases: None
• Description: speckle-type POZ protein-like [Source:HGNC Symbol;Acc:27934]

Sequence

>retro_pabe_2440
TGTTATACACGGGTCAAAGTAGTAAAATGTTCAACACGTAGACCATTAATAACTTCATTTTTTGTCAAGAGGAAATGGTG
AGGAGGTAAAAAGTTCCACATTTTCGCCTGGCCCAGTGACAAAATGAAATGGTGCCTGAGGGTAAACCCAAAGGGATTAG
ATAATGAAAGTGAAGACAACTTGTCCTTATATTTGCTTTTAGTCAGATGCCCCAAAAGTGAAGTGTGAGCAAAACTCAAA
TTTTCTCTTCTGAACTCCAAAATGGAAGAAAGAAAAGCAATGGAAAGTCAAAGGCATATCAAGTTGTGCAAGGGAAGGAC
TGGGATTTTTAAAAAAATCATTAGAAGGGACCTTTAGCTTGAGGAGGCTAATGGTCTTTTACCAGATGACAAGCTTACAT
TATTTTGTGAGGTGATTGTGGTCCAAGATTCAGTAAATATATCAGGACATACTAATACAAATACTTTGAAGGTGGCTGAG
TATTGACTAGGAGAAGATTTAGGTAATCTCTAGGATAACACAAGATTTACAGACTGCAGTTTTTTGTGAGAGAACAAGAG
TTTAAAGCTCATATAAATCTGCTTGTACCTCCATCCCCAGTTTTTAATGCCATGTTTGAACATGAAATGGAATAAAGCAT
AAAGAATCGAGTGGAAATAAATGATTTAGATCCTGATGTTTTTAAAGAAATGATGAGATTC

Alignment

ORF - retro_pabe_2440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.25 %
• Parental protein coverage: 59.95 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  CYTQVKVV-KFSYMWTINNFSFCREEM-GEVLKSSTFSSGP-SDKMKWCLRVNPKGLDDESKDYLSLYLL
          CYT.VKVV.K.....TINNF.FC.EEM.GE..KSSTFS.GP.SDKMKWCLRVNPKGLD.ES.D.LSLYLL
Retrocopy CYTRVKVV<KMFNT*TINNFIFCQEEM<GEEVKSSTFSPGP<SDKMKWCLRVNPKGLDNESEDNLSLYLL

Parental  LVSCPKSEVRAKFKFSLLNAKREETKAMESQR-AYRFVQGKDWGF-KKFIRRDFLLDEANGLLPDDKLTL
          LV.CPKSEV.AK.KFSLLN.K.EE.KAMESQR.AY..VQGKDW.F.KK.IRRD..L.EANGLLPDDKLTL
Retrocopy LVRCPKSEV*AKLKFSLLNSKMEERKAMESQR<AYQVVQGKDWDF>KKIIRRDL*LEEANGLLPDDKLTL

Parental  FCEVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWENTRFTDCS-FFVRGQEFKAHKSVLAARSPVFN
          FCEV.VVQDSVNISGHTNTNTLKV.E..L.EDLGNL..NTRFTDCS.FFVR.QEFKAH...L...SPVFN
Retrocopy FCEVIVVQDSVNISGHTNTNTLKVAEY*LGEDLGNL*DNTRFTDCS<FFVREQEFKAHINLLVPPSPVFN

Parental  AMFEHEMEESKKNRVEINDLDPEVFKEMMRF
          AMFEHEME.S.KNRVEINDLDP.VFKEMMRF
Retrocopy AMFEHEME*SIKNRVEINDLDPDVFKEMMRF

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	12.00 RPM
SRP007412_cerebellum	0.00 RPM	22.74 RPM
SRP007412_heart	0.00 RPM	7.29 RPM
SRP007412_kidney	0.00 RPM	13.39 RPM
SRP007412_liver	0.00 RPM	7.59 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2440 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2440 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884, retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439, retro_pabe_2440 , retro_pabe_2599,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991, retro_ptro_2054,