RetrogeneDB ID: retro_pabe_3750

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:47497335..47497986(-)
• Located in intron of: ENSPPYG00000020279

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_3750
ATCAACCAATTCTTCGGGAAAGTGAAACCCAAGGCTCCACTGCCCAGCCTGACTGACTGCATTGACACGGTGGACAGCAG
GGCAGAATCCAAGAAGATTTCTTGATTGGATGCTGAGCTAGTGAAGTATAAGGATCAGATCAAGAAGATGAGAGAGGGTC
CTGCAAAGAGTATGGTTCAGCAGAAAGCCTCGCGAGTTTTAAAGCAAAAGTGGATGTATGAGCAGCAGCAGGACAATCTT
GCCCAACAGTCATTCAACGTGGAACAAGCCAATTATACTATCCAGTCATTGAAGGACACCAAGACCACGGTTGATGCTAT
GAAACTGGGAGTAAAGGAAATGAAGAAGGCATACAAGCAAGTGAAAATCGACCAGATTGAGGATTTACGAGACCAGCTAG
AGGATATGATGGAAGATGTAAATGAAATCCAAGAAGCACTGAGTCGCAGTTATGGCACACCAGAACTGGATGAAGATGAC
CTAGAAGCAAAGTTGGATGCACTGGGTGATGAGCTTCTGGCTGATGAAGACAGTTCTTATTTGGATGAGACAGCATCTGC
ACCTGCAATTCCAGAAGGTGTTCCCACTGATACAAAAAACAAGGATGGAGTTCTGGTGGATGAATTTGGATTGCCACAGA
TCCCTACTTCA

Alignment

ORF - retro_pabe_3750 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNRLFGKAKPKAPPPSLTDCIGTVDSRAESIDKKISRLDAELVKYKDQIKKMREGPAKNMVKQKALRVLK
          .N..FGK.KPKAP.PSLTDCI.TVDSRAES..KKIS.LDAELVKYKDQIKKMREGPAK.MV.QKA.RVLK
Retrocopy INQFFGKVKPKAPLPSLTDCIDTVDSRAES--KKIS*LDAELVKYKDQIKKMREGPAKSMVQQKASRVLK

Parental  QKRMYEQQRDNLAQQSFNMEQANYTIQSLKDTKTTVDAMKLGVKEMKKAYKQVKIDQIEDLQDQLEDMME
          QK.MYEQQ.DNLAQQSFN.EQANYTIQSLKDTKTTVDAMKLGVKEMKKAYKQVKIDQIEDL.DQLEDMME
Retrocopy QKWMYEQQQDNLAQQSFNVEQANYTIQSLKDTKTTVDAMKLGVKEMKKAYKQVKIDQIEDLRDQLEDMME

Parental  DANEIQEALSRSYGTPELDEDDLEAELDALGDELLADEDSSYLDEAASAPAIPEGVPTDTKNKDGVLVDE
          D.NEIQEALSRSYGTPELDEDDLEA.LDALGDELLADEDSSYLDE.ASAPAIPEGVPTDTKNKDGVLVDE
Retrocopy DVNEIQEALSRSYGTPELDEDDLEAKLDALGDELLADEDSSYLDETASAPAIPEGVPTDTKNKDGVLVDE

Parental  FGLPQIPAS
          FGLPQIP.S
Retrocopy FGLPQIPTS

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	1.38 RPM	52.91 RPM
SRP007412_cerebellum	2.80 RPM	50.46 RPM
SRP007412_heart	0.69 RPM	28.42 RPM
SRP007412_kidney	1.43 RPM	47.47 RPM
SRP007412_liver	0.92 RPM	28.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3750 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3750 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3750 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4822
Pan troglodytes	retro_ptro_3210
Macaca mulatta	retro_mmul_2573

---

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,