RetrogeneDB ID: retro_pabe_239

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:46405122..46405736(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP5
• Ensembl ID: ENSPPYG00000019137
• Aliases: None
• Description: Charged multivesicular body protein 5 [Source:UniProtKB/Swiss-Prot;Acc:Q5RBR3]

Sequence

>retro_pabe_239
AAGGCTCCGCTGCCCAGCCTGAATGACTGCATTGGCATGGTGGACAGCAGGGCAGAATCCACTGACAAGATTTCTAGATT
GGATGCTGAGCTAGTGAAGTATAAGGACCAGATCAAGATGAGAGGGGGTCCTACAAAGAATATGATTACGCAGAAAGCCT
TGCAAGTTTTAAAACAAAAGTGGATGTATGAGCAGCATCAGGACAATCACACCCAATAGTCATTCAACATGAAACAAGTC
AATTACACCTTCCAGTCATTGAAGGATACCAAGACCACAGTTGATGCTATGAAACTGGGAGCAAAGGAAATAAAGGTAGA
CAAGCAAGTGAAAACTGACCAGATTGAGAATTTACAAGACCAGCTGGTGGACATGATGGAAGATGCAAATGAAATCCAAG
AAGCACTGAGTCGCAGTTATGGCAGCCCAGAATTAGATGAAGACGACCTAGAAGCAGAGTTGGATACACTGGGTGATGAG
CTTGTGGCTGACCAAGACAGTTCTATTTAGATGAAGCAGCATCTGCACCTGCAATTCCAGAAGGTGTTCCCAATGTCACA
AAAAACAAGGATGGAGTTCTAGTGGATGAATTTGGATTGCCACAGATCCCTGCT

Alignment

ORF - retro_pabe_239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.25 %
• Parental protein coverage: 94.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAPPPSLTDCIGTVDSRAESIDKKISRLDAELVKYKDQIKKMREGPAKNMVKQKALRVLKQKRMYEQQRD
          KAP.PSL.DCIG.VDSRAES.DK.ISRLDAELVKYKDQIK.MR.GP.KNM..QKAL.VLKQK.MYEQ..D
Retrocopy KAPLPSLNDCIGMVDSRAESTDK-ISRLDAELVKYKDQIK-MRGGPTKNMITQKALQVLKQKWMYEQHQD

Parental  NLAQQSFNMEQANYTIQSLKDTKTTVDAMKLGVKEMKKAYKQVKIDQIEDLQDQLEDMMEDANEIQEALS
          N..Q.SFNM.Q.NYT.QSLKDTKTTVDAMKLG.KE.K...KQVK.DQIE.LQDQL.DMMEDANEIQEALS
Retrocopy NHTQ*SFNMKQVNYTFQSLKDTKTTVDAMKLGAKEIK-VDKQVKTDQIENLQDQLVDMMEDANEIQEALS

Parental  RSYGTPELDEDDLEAELDALGDELLADEDSS-YLDEAASAPAIPEGVPTDTKNKDGVLVDEFGLPQIPA
          RSYG.PELDEDDLEAELD.LGDEL.AD.DSS.YLDEAASAPAIPEGVP..TKNKDGVLVDEFGLPQIPA
Retrocopy RSYGSPELDEDDLEAELDTLGDELVADQDSS<YLDEAASAPAIPEGVPNVTKNKDGVLVDEFGLPQIPA

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	52.91 RPM
SRP007412_cerebellum	0.61 RPM	50.46 RPM
SRP007412_heart	0.06 RPM	28.42 RPM
SRP007412_kidney	0.10 RPM	47.47 RPM
SRP007412_liver	0.12 RPM	28.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_239 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_239 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_494
Pan troglodytes	retro_ptro_373

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012672	1 retrocopy	retro_chof_2045,
Callithrix jacchus	ENSCJAG00000008104	2 retrocopies	retro_cjac_2868, retro_cjac_4159,
Cavia porcellus	ENSCPOG00000003467	2 retrocopies	retro_cpor_1221, retro_cpor_1306,
Dipodomys ordii	ENSDORG00000006280	2 retrocopies	retro_dord_292, retro_dord_764,
Echinops telfairi	ENSETEG00000001424	1 retrocopy	retro_etel_2126,
Homo sapiens	ENSG00000086065	2 retrocopies	retro_hsap_4822, retro_hsap_494,
Microcebus murinus	ENSMICG00000012113	2 retrocopies	retro_mmur_369, retro_mmur_843,
Myotis lucifugus	ENSMLUG00000011045	1 retrocopy	retro_mluc_954,
Macaca mulatta	ENSMMUG00000020149	1 retrocopy	retro_mmul_2573,
Monodelphis domestica	ENSMODG00000004012	2 retrocopies	retro_mdom_2002, retro_mdom_595,
Mus musculus	ENSMUSG00000028419	1 retrocopy	retro_mmus_1469,
Nomascus leucogenys	ENSNLEG00000005158	2 retrocopies	retro_nleu_2197, retro_nleu_2420,
Otolemur garnettii	ENSOGAG00000000774	6 retrocopies	retro_ogar_2072, retro_ogar_2190, retro_ogar_2386, retro_ogar_2504, retro_ogar_2509, retro_ogar_916,
Pongo abelii	ENSPPYG00000019137	2 retrocopies	retro_pabe_239 , retro_pabe_3750,
Pan troglodytes	ENSPTRG00000020857	2 retrocopies	retro_ptro_3210, retro_ptro_373,
Rattus norvegicus	ENSRNOG00000008672	1 retrocopy	retro_rnor_2614,
Ictidomys tridecemlineatus	ENSSTOG00000026573	1 retrocopy	retro_itri_424,
Tupaia belangeri	ENSTBEG00000003486	5 retrocopies	retro_tbel_1626, retro_tbel_1894, retro_tbel_2407, retro_tbel_3364, retro_tbel_3494,
Tursiops truncatus	ENSTTRG00000010575	1 retrocopy	retro_ttru_338,