RetrogeneDB ID: retro_pabe_3101

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:135186206..135186990(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2R5C
• Ensembl ID: ENSPPYG00000006152
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B', gamma [Source:HGNC Symbol;Acc:9311]

Sequence

>retro_pabe_3101
GAGAGAGCTTTTCCTAAAATCAGCCTTTGCAGAATCTATGGGAAATTCTTAGGCTTGAGAGCTTATATCGGAAAGCAGAT
ACATAATATATTTTATAGGTTTATTTATGAAGCAGAGCATCATGATGACATAGCAGAGTTACTAGATACATTGGGAAATA
TGATTAATGGATTTGTTTTACCACTAAAAGAAGAGCACAGATTTTCTTATTCAAGGGTTTGCACAAAGTGAAATCTCTGA
GAGTCTACCATCCCCAGCTGGCATATTGTGTAGTACAGTTTTTAGAAAAGGATAGCACCCTCACTGCATCAATGGTGATG
GCACTTCTCAAATATGGGCCAAAGTCTTACAGTCCAAAAGAAGTAATTTTCTTAAACAAATTAGAAGAAATTTTAGATAT
AATTGAACCATTGGAATTTGGAAGATCATGGAACCTCTCTTCTGGCAGCTAGCCAAATGTGTCTCCAGCTCACACTTCCA
GGTGGCAGAGCAAGTGCTCTATTACCGGAATAATGAATACATTATGAGCTTAATCAGTAACAGCATAGCAAAGATTCTGC
TGATCATGTTTCCATGCTTGTACTGCAATTCAAAGACCCATTGGAACAAGACAATACGTGGCTTGATATCCAACACACTG
AAGCTCTTCATGCAGATGAACCAAAAGCTATTTAATGACTGTACCTAACTGTTCAAAGCAGAGAAACTGAAAGAGAAGCT
AAAAATGAAAGAACAGGAAGAAGCATTGGTTAAAATAGAAAATCTAACCAAAGCTAATCACCAG

Alignment

ORF - retro_pabe_3101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.65 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALPLKEEHK-IF
          ER.F.K..L.RIYGKFLGLRAYI.KQI.NIFYRFIYE.EHH..IAELL..LG..INGF.LPLKEEH..IF
Retrocopy ERAFPKISLCRIYGKFLGLRAYIGKQIHNIFYRFIYEAEHHDDIAELLDTLGNMINGFVLPLKEEHR<IF

Parental  LLKVLLPLHKVKSLSVYHPQLAYCVVQFLEKDSTLTEPVVMALLKYWPKTHSPKEVMFLNELEEILDVIE
          L.K....LHKVKSL.VYHPQLAYCVVQFLEKDSTLT...VMALLKY.PK..SPKEV.FLN.LEEILD.IE
Retrocopy LFK---GLHKVKSLRVYHPQLAYCVVQFLEKDSTLTASMVMALLKYGPKSYSPKEVIFLNKLEEILDIIE

Parental  PSEF-VKIMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAAKILPIMFPSLYRNSKTHWNKT
          P.EF..KIMEPLF.QLAKCVSS.HFQVAE..LYY.NNEYIMSLIS...AKIL.IMFP.LY.NSKTHWNKT
Retrocopy PLEF<WKIMEPLFWQLAKCVSSSHFQVAEQVLYYRNNEYIMSLISNSIAKILLIMFPCLYCNSKTHWNKT

Parental  IHGLIYNALKLFMEMNQKLFDDCTQQFKAEKLKEKLKMKEREEAWVKIENLAKANPQ
          I.GLI.N.LKLFM.MNQKLF.DCT..FKAEKLKEKLKMKE.EEA.VKIENL.KAN.Q
Retrocopy IRGLISNTLKLFMQMNQKLFNDCT*LFKAEKLKEKLKMKEQEEALVKIENLTKANHQ

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	69.28 RPM
SRP007412_cerebellum	0.00 RPM	53.63 RPM
SRP007412_heart	0.00 RPM	52.38 RPM
SRP007412_kidney	0.00 RPM	51.61 RPM
SRP007412_liver	0.00 RPM	50.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3101 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3101 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3796

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000078304	2 retrocopies	retro_hsap_2649, retro_hsap_3796,
Nomascus leucogenys	ENSNLEG00000015727	2 retrocopies	retro_nleu_1125, retro_nleu_655,
Otolemur garnettii	ENSOGAG00000006274	1 retrocopy	retro_ogar_1944,
Pongo abelii	ENSPPYG00000006152	3 retrocopies	retro_pabe_2322, retro_pabe_2414, retro_pabe_3101 ,
Pongo abelii	ENSPPYG00000016625	1 retrocopy	retro_pabe_1434,
Pan troglodytes	ENSPTRG00000006734	1 retrocopy	retro_ptro_1784,