RetrogeneDB ID: retro_ptro_3210

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:47232758..47233415(-)
• Located in intron of: ENSPTRG00000021832

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP5
• Ensembl ID: ENSPTRG00000020857
• Aliases: None
• Description: None

Sequence

>retro_ptro_3210
ATCAACCAATTCTTCGGGAAAGTGAAACCCAAGGCTCCACTGCCCAGCCTGACTGACTGCATTGACACGGTGGACAGCAG
GGCAGAATCCATTGACAAGAAGATTTCTCGATTGGATGCTGAGCTAGTGAAGTATAAGGATCAGATCAAGAAGATGAGAG
AGGGTCCTACAAAGAGTATGGTTAAGCAGAAAGCCTCGTGAGTTTTAAAGCAAAAGTGGATGTATGAGCAGCAGCAGGGC
AATCTTGCCCAATAGTCATTCAACATGGAACAAGCCAATTATACCATCCAGTCATTGAAGGACACCAAGACCACGGTTGA
TGCTATGAAACTGGGAGTAAAGGAAATGAAGAAGGCATACAAGCAAGTGAAAATCGACCAGATTGAGGATTTACGAGACC
AGCTAGAGGATATGATGGAAGATGCAAATGAAATCCAAGAAGCACTGAGTCGCAGTTATGGCACACCAGAACTGGATGAA
GATGACCTAGAAGCAAAGTTGGATGCACTGGGTGATGAGCTTCTGGCTGATGAAGACAGTTCTTATTTGGATGAGACAGC
ATCTGCACCTGCAATTCCGGAAGGTGTTCCCACTGATACGAAAAACAAGGATGGAGTTCTGGTGGATGAATTTGGATTGC
CACAGATCCCTACTTCA

Alignment

ORF - retro_ptro_3210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNRLFGKAKPKAPPPSLTDCIGTVDSRAESIDKKISRLDAELVKYKDQIKKMREGPAKNMVKQKALRVLK
          .N..FGK.KPKAP.PSLTDCI.TVDSRAESIDKKISRLDAELVKYKDQIKKMREGP.K.MVKQKA..VLK
Retrocopy INQFFGKVKPKAPLPSLTDCIDTVDSRAESIDKKISRLDAELVKYKDQIKKMREGPTKSMVKQKAS*VLK

Parental  QKRMYEQQRDNLAQQSFNMEQANYTIQSLKDTKTTVDAMKLGVKEMKKAYKQVKIDQIEDLQDQLEDMME
          QK.MYEQQ..NLAQ.SFNMEQANYTIQSLKDTKTTVDAMKLGVKEMKKAYKQVKIDQIEDL.DQLEDMME
Retrocopy QKWMYEQQQGNLAQ*SFNMEQANYTIQSLKDTKTTVDAMKLGVKEMKKAYKQVKIDQIEDLRDQLEDMME

Parental  DANEIQEALSRSYGTPELDEDDLEAELDALGDELLADEDSSYLDEAASAPAIPEGVPTDTKNKDGVLVDE
          DANEIQEALSRSYGTPELDEDDLEA.LDALGDELLADEDSSYLDE.ASAPAIPEGVPTDTKNKDGVLVDE
Retrocopy DANEIQEALSRSYGTPELDEDDLEAKLDALGDELLADEDSSYLDETASAPAIPEGVPTDTKNKDGVLVDE

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	0.18 RPM	51.01 RPM
SRP007412_cerebellum	0.25 RPM	59.11 RPM
SRP007412_heart	0.17 RPM	47.83 RPM
SRP007412_kidney	0.26 RPM	63.76 RPM
SRP007412_liver	0.23 RPM	34.83 RPM
SRP007412_testis	0.53 RPM	54.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3210 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3210 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4822
Pongo abelii	retro_pabe_3750
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,