RetrogeneDB ID: retro_ptro_301

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:53441268..53441772(-)
• Located in intron of: ENSPTRG00000000748

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRAS2
• Ensembl ID: ENSPTRG00000003383
• Aliases: None
• Description: related RAS viral (r-ras) oncogene homolog 2 [Source:HGNC Symbol;Acc:17271]

Sequence

>retro_ptro_301
TCCTATTTTGTAACGGATTATGATCCAACCATTGAAGATTCTTACACAAAGCAGTGTGTGATAGATGACAGAGCAGCCCG
GCTAGATATTTTGGATACAGCAGGACAAGAAGAGTTTGGAGCCATGAGAGAACAGTATATGAGGACTGGCGAGGGCTTCC
TGTTGGTCTTTTCAGTCACAGATAGAGGCAGTTTTGAAGAAATCTATAAGTTTCAAAGACAGATTCTCAGAGTAAAGGAT
CGTGATGAGTTCCCAATGATTTTAATTGGTAATAAAGCAGATCTGGATCATCAAAGACAGGTAACACAGGAAGAAGGACG
GCAGTTAGCACGGCAACTTAAGGTAACATACATGAAGGCATCAGCAAAGATTAGGATGAATGTAGATCAAGCTTTCCATG
AACTTGTCCGGGTTATCAGGAAATTTCAAGAGCAGGAATGTCCTCCTTCACCAGAACCAACACGGAAAGAAAAAGACAAG
AAAGGCTGCCATTGTGTTATTTTC

Alignment

ORF - retro_ptro_301 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.81 %
• Parental protein coverage: 82.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQYMRTGEGFLLVFSVTDRGSFEEIYK
          SYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQYMRTGEGFLLVFSVTDRGSFEEIYK
Retrocopy SYFVTDYDPTIEDSYTKQCVIDDRAARLDILDTAGQEEFGAMREQYMRTGEGFLLVFSVTDRGSFEEIYK

Parental  FQRQILRVKDRDEFPMILIGNKADLDHQRQVTQEEGQQLARQLKVTYMEASAKIRMNVDQAFHELVRVIR
          FQRQILRVKDRDEFPMILIGNKADLDHQRQVTQEEG.QLARQLKVTYM.ASAKIRMNVDQAFHELVRVIR
Retrocopy FQRQILRVKDRDEFPMILIGNKADLDHQRQVTQEEGRQLARQLKVTYMKASAKIRMNVDQAFHELVRVIR

Parental  KFQEQECPPSPEPTRKEKDKKGCHCVIF
          KFQEQECPPSPEPTRKEKDKKGCHCVIF
Retrocopy KFQEQECPPSPEPTRKEKDKKGCHCVIF

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	3.29 RPM	3.95 RPM
SRP007412_cerebellum	1.61 RPM	4.52 RPM
SRP007412_heart	0.64 RPM	11.95 RPM
SRP007412_kidney	0.47 RPM	20.29 RPM
SRP007412_liver	1.93 RPM	13.39 RPM
SRP007412_testis	0.11 RPM	14.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_301 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_301 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_301 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_390

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002367	1 retrocopy	retro_amel_947,
Bos taurus	ENSBTAG00000011905	1 retrocopy	retro_btau_1295,
Choloepus hoffmanni	ENSCHOG00000003135	7 retrocopies	retro_chof_111, retro_chof_1639, retro_chof_2065, retro_chof_2644, retro_chof_2706, retro_chof_389, retro_chof_521,
Dasypus novemcinctus	ENSDNOG00000011828	6 retrocopies	retro_dnov_124, retro_dnov_1458, retro_dnov_1708, retro_dnov_1779, retro_dnov_2331, retro_dnov_988,
Erinaceus europaeus	ENSEEUG00000000240	1 retrocopy	retro_eeur_531,
Felis catus	ENSFCAG00000009578	1 retrocopy	retro_fcat_386,
Homo sapiens	ENSG00000133818	1 retrocopy	retro_hsap_390,
Gorilla gorilla	ENSGGOG00000004759	1 retrocopy	retro_ggor_1813,
Myotis lucifugus	ENSMLUG00000007005	1 retrocopy	retro_mluc_1264,
Macaca mulatta	ENSMMUG00000000664	2 retrocopies	retro_mmul_1604, retro_mmul_965,
Monodelphis domestica	ENSMODG00000028397	2 retrocopies	retro_mdom_1254, retro_mdom_577,
Oryctolagus cuniculus	ENSOCUG00000011362	1 retrocopy	retro_ocun_1645,
Otolemur garnettii	ENSOGAG00000027655	1 retrocopy	retro_ogar_1081,
Ochotona princeps	ENSOPRG00000005967	1 retrocopy	retro_opri_2,
Pongo abelii	ENSPPYG00000025912	1 retrocopy	retro_pabe_3043,
Pan troglodytes	ENSPTRG00000003383	2 retrocopies	retro_ptro_1747, retro_ptro_301 ,
Rattus norvegicus	ENSRNOG00000012258	1 retrocopy	retro_rnor_750,
Ictidomys tridecemlineatus	ENSSTOG00000022169	1 retrocopy	retro_itri_1457,
Tupaia belangeri	ENSTBEG00000001292	1 retrocopy	retro_tbel_3234,
Tursiops truncatus	ENSTTRG00000010419	1 retrocopy	retro_ttru_1218,
Vicugna pacos	ENSVPAG00000008814	1 retrocopy	retro_vpac_165,