RetrogeneDB ID: retro_ptro_1484

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:19341443..19342049(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: E2F6
• Ensembl ID: ENSPTRG00000011661
• Aliases: None
• Description: Pan troglodytes E2F transcription factor 6 (E2F6), mRNA. [Source:RefSeq mRNA;Acc:NM_001242344]

Sequence

>retro_ptro_1484
AAATCTGCTCCCGGGGGTATTCTTGACTTAAACAAGGTTGCAACGAAACTGGGAGTCCGAAAGCGGAGAGTGTATGACAT
CACCAGTGTCTTAGATGGAATCGACCTCGTTGAAAAGAAATCCAAGAACCATATTAGATGGATAGGATCTGATCTTAGCA
ATTTTGGAGCAGTTCCCCAACAAAAGAAGCTACAGGAGGAACTTTCTGACTTATCAGCAATGGAAGATGCTTTGGATGAG
TTAATTAAGGATTGTGCTCAGCAGCTGTTTGAGTTAACAGATGACAAAGAAAATGAAAGACTAGCATATGTGACCTATCA
AGACATTCATAGCATTCAGGCCTTCCATGAACAGATCGTCATTGCAGTTAAAGCTCCAGCAGAAACCAGATTGGATGTTC
CAGCTCCCAGAGAAGACTCTATCACAGTGCACATAAGGAGCACCAACGGACCTATCGATGTCTATTTGTGAGAAGTGGAG
CAGGGTCAGACCAGTAACAAAAGGTCTGAAGGTGTCGGGACCTCTTCATCTGAGAGCACTCATCCAGAAGGCCCTGAGGA
AGAAGAAAATCCTCAGCAAAGTGAAGAATTGCTTGAAGTAAGCAAC

Alignment

ORF - retro_ptro_1484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.51 %
• Parental protein coverage: 71.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSAPGGILDLNKVATKLGVRKRRVYDITNVLDGIDLVEKKSKNHIRWIGSDLSNFGAVPQQKKLQEELSD
          .SAPGGILDLNKVATKLGVRKRRVYDIT.VLDGIDLVEKKSKNHIRWIGSDLSNFGAVPQQKKLQEELSD
Retrocopy KSAPGGILDLNKVATKLGVRKRRVYDITSVLDGIDLVEKKSKNHIRWIGSDLSNFGAVPQQKKLQEELSD

Parental  LSAMEDALDELIKDCAQQLFELTDDKENERLAYVTYQDIHSIQAFHEQIVIAVKAPAETRLDVPAPREDS
          LSAMEDALDELIKDCAQQLFELTDDKENERLAYVTYQDIHSIQAFHEQIVIAVKAPAETRLDVPAPREDS
Retrocopy LSAMEDALDELIKDCAQQLFELTDDKENERLAYVTYQDIHSIQAFHEQIVIAVKAPAETRLDVPAPREDS

Parental  ITVHIRSTNGPIDVYLCEVEQGQTSNKRSEGVGTSSSESTHPEGPEEEENPQQSEELLEVSN
          ITVHIRSTNGPIDVYL.EVEQGQTSNKRSEGVGTSSSESTHPEGPEEEENPQQSEELLEVSN
Retrocopy ITVHIRSTNGPIDVYL*EVEQGQTSNKRSEGVGTSSSESTHPEGPEEEENPQQSEELLEVSN

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	0.14 RPM	11.30 RPM
SRP007412_cerebellum	0.00 RPM	8.60 RPM
SRP007412_heart	0.00 RPM	10.75 RPM
SRP007412_kidney	0.00 RPM	7.40 RPM
SRP007412_liver	0.00 RPM	5.30 RPM
SRP007412_testis	0.11 RPM	6.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1484 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1484 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1484 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2572
Homo sapiens	retro_hsap_2547
Homo sapiens	retro_hsap_2542

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000048286	1 retrocopy	retro_btau_1820,
Callithrix jacchus	ENSCJAG00000006910	1 retrocopy	retro_cjac_178,
Dasypus novemcinctus	ENSDNOG00000000258	1 retrocopy	retro_dnov_187,
Homo sapiens	ENSG00000169016	4 retrocopies	retro_hsap_2542, retro_hsap_2547, retro_hsap_2572, retro_hsap_4906,
Macropus eugenii	ENSMEUG00000007957	4 retrocopies	retro_meug_1169, retro_meug_860, retro_meug_882, retro_meug_893,
Myotis lucifugus	ENSMLUG00000003384	1 retrocopy	retro_mluc_864,
Macaca mulatta	ENSMMUG00000023225	1 retrocopy	retro_mmul_87,
Nomascus leucogenys	ENSNLEG00000014134	1 retrocopy	retro_nleu_2351,
Pongo abelii	ENSPPYG00000012646	1 retrocopy	retro_pabe_1,
Pan troglodytes	ENSPTRG00000011661	2 retrocopies	retro_ptro_1484 , retro_ptro_3272,
Pan troglodytes	ENSPTRG00000023584	2 retrocopies	retro_ptro_1217, retro_ptro_1731,
Ictidomys tridecemlineatus	ENSSTOG00000003316	1 retrocopy	retro_itri_135,