RetrogeneDB ID: retro_pabe_3441

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:102011439..102012303(+)
• Located in intron of: ENSPPYG00000019474

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPDC1
• Ensembl ID: ENSPPYG00000001248
• Aliases: None
• Description: DEP domain containing 1 [Source:HGNC Symbol;Acc:22949]

Sequence

>retro_pabe_3441
TTATGGAATGAAATTACTACATCTTTTCAAGCAGGAATGCCTCTAAGAAAACACAGACAACACTTAAAAAATATGGCAGT
TGTTTCACAGCAGGACAAGCAGCGGATTGGCTTTATGACCTATTAAGAAATAATAGCAATTTTCATCCTAAAGTTACAAG
GCAACAGACTATCCAACTGTTGAGGAAATTTCTTGAGAATCATGTAATTGAAGATATCAAAGGCAGGTGGGGATCAGAAA
ATGTTGATGATACTAACCAGCTCTTCAGATTTCCTGCAACTTAGCCATTTGAAACTCTGCCACGAAGACATCTAGAATTG
AGAAAAAAACAACATAGAGAACTTTTCCAAAGATAAAGATAGTATTTTTAAATGACGAAACTTATCTCATAGAACTCCTA
AAAAGCATGGATTACATTTATCTCAGGAAAATTCCGAGAAAATAAAGCATGAAATAATCAATGAAGATCAAGAAAATGTA
GTTGATAATAGAAAACTAAGCCAGGAAGATGTTGAAGAAATTTGGAGATATGTTATTCTGATCTACCTGCAAACCATTTT
AGGTGTGCCATCCCTAGAAGAAGTCATAAATCCAAAACAAGTAATTCCCCAATATATAATGTACAACATGGCCAATACAA
GTAAACATGGAGTAGTTATACTACAAAACAAATCAGATGACCTCCCTCACTGGGTATTATGTGCCATGAAGTGCCTAGCA
AATTGGCCAAGAAGTGATGATATGAATAATCCAACATATGTTGGATTTGAACAAGATATATTCAGCACAATCACAAATTA
TTTTCTAGATCTCCTTGAACCTCTTCTTACTTTTGAATATTACGAATTATTTATGAACATTTTG

Alignment

ORF - retro_pabe_3441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 54.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LWNEVTTSFRAGMPLRKHRQHFK-KYGNCFTAGEAVDWLYDLLRNNSNFGPEVTRQQTIQLLRKFLKNHV
          LWNE.TTSF.AGMPLRKHRQH.K.KYG.CFTAG.A.DWLYDLLRNNSNF.P.VTRQQTIQLLRKFL.NHV
Retrocopy LWNEITTSFQAGMPLRKHRQHLK<KYGSCFTAGQAADWLYDLLRNNSNFHPKVTRQQTIQLLRKFLENHV

Parental  IEDIKGRWGSENVDDNNQLFRFPATSPLKTLPRRHLELRK-NNVENFSKDKDSIFKLRNLSRRTPKRHGL
          IEDIKGRWGSENVDD.NQLFRFPAT.P..TLPRRHLELRK.NN.ENFSKDKDSIFK.RNLS.RTPK.HGL
Retrocopy IEDIKGRWGSENVDDTNQLFRFPAT*PFETLPRRHLELRK>NNIENFSKDKDSIFK*RNLSHRTPKKHGL

Parental  HLSQENGEKIKHEIINEDQENAIDNRELSQEDVEEVWRYVILIYLQTILGVPSLEEVINPKQVIPQYIMY
          HLSQEN.EKIKHEIINEDQEN..DNR.LSQEDVEE.WRYVILIYLQTILGVPSLEEVINPKQVIPQYIMY
Retrocopy HLSQENSEKIKHEIINEDQENVVDNRKLSQEDVEEIWRYVILIYLQTILGVPSLEEVINPKQVIPQYIMY

Parental  NMANTSKHGVVILQNKSDDLPHWVLSAMKCLANWPRSNDMNNPTYAGFERDVFRTIADYFLDLPEPLLTF
          NMANTSKHGVVILQNKSDDLPHWVL.AMKCLANWPRS.DMNNPTY.GFE.D.F.TI..YFLDL.EPLLTF
Retrocopy NMANTSKHGVVILQNKSDDLPHWVLCAMKCLANWPRSDDMNNPTYVGFEQDIFSTITNYFLDLLEPLLTF

Parental  EYYELFVNIL
          EYYELF.NIL
Retrocopy EYYELFMNIL

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	0.22 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.06 RPM	0.33 RPM
SRP007412_kidney	0.03 RPM	0.03 RPM
SRP007412_liver	0.00 RPM	0.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3441 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3441 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3441 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013839	1 retrocopy	retro_cpor_735,
Homo sapiens	ENSG00000024526	2 retrocopies	retro_hsap_1545, retro_hsap_4206,
Gorilla gorilla	ENSGGOG00000016316	1 retrocopy	retro_ggor_1176,
Macaca mulatta	ENSMMUG00000017766	1 retrocopy	retro_mmul_1176,
Mus musculus	ENSMUSG00000028175	1 retrocopy	retro_mmus_3028,
Nomascus leucogenys	ENSNLEG00000009334	1 retrocopy	retro_nleu_2931,
Otolemur garnettii	ENSOGAG00000000934	1 retrocopy	retro_ogar_1907,
Pongo abelii	ENSPPYG00000001248	1 retrocopy	retro_pabe_3441 ,
Pan troglodytes	ENSPTRG00000000847	2 retrocopies	retro_ptro_1041, retro_ptro_2855,