RetrogeneDB ID: retro_ptro_1170

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:24766100..24766319(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000038874
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBL5
• Ensembl ID: ENSPTRG00000010451
• Aliases: None
• Description: None

Sequence

>retro_ptro_1170
ATGATCGAGGTTGTTTGCAACGACCGTCTGGGGAAAAAGGTCCACGTTAAATGCAACACGGATGATACCATCAGGGACCT
TAAGAAGCTGATTGCAGCCTAAACTGGCATCCGTTGGAACAAGATTGTCCTGAAGAAGTGGTACACAATTTTTAAGGACC
ATGTGTCTCTGGGGGACTATGAAATCCACAATGGGATGAACCTGGAGCTTTATTATCAA

Alignment

ORF - retro_ptro_1170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLEL
          MIEVVCNDRLGKKV.VKCNTDDTI.DLKKLIAA.TG.RWNKIVLKKWYTIFKDHVSLGDYEIH.GMNLEL
Retrocopy MIEVVCNDRLGKKVHVKCNTDDTIRDLKKLIAA*TGIRWNKIVLKKWYTIFKDHVSLGDYEIHNGMNLEL

Parental  YYQ
          YYQ
Retrocopy YYQ

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	0.23 RPM	65.78 RPM
SRP007412_cerebellum	0.54 RPM	44.02 RPM
SRP007412_heart	0.09 RPM	50.10 RPM
SRP007412_kidney	0.10 RPM	92.05 RPM
SRP007412_liver	0.00 RPM	61.21 RPM
SRP007412_testis	0.42 RPM	118.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1170 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1170 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1170 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1821
Pongo abelii	retro_pabe_1489

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006097	1 retrocopy	retro_cjac_1394,
Dasypus novemcinctus	ENSDNOG00000006384	5 retrocopies	retro_dnov_1858, retro_dnov_196, retro_dnov_2470, retro_dnov_2590, retro_dnov_860,
Homo sapiens	ENSG00000198258	3 retrocopies	retro_hsap_1821, retro_hsap_2798, retro_hsap_3154,
Gorilla gorilla	ENSGGOG00000005999	1 retrocopy	retro_ggor_173,
Loxodonta africana	ENSLAFG00000012892	2 retrocopies	retro_lafr_1245, retro_lafr_699,
Macropus eugenii	ENSMEUG00000015506	2 retrocopies	retro_meug_300, retro_meug_304,
Myotis lucifugus	ENSMLUG00000027369	2 retrocopies	retro_mluc_1516, retro_mluc_1766,
Macaca mulatta	ENSMMUG00000007877	2 retrocopies	retro_mmul_1437, retro_mmul_1996,
Mus musculus	ENSMUSG00000084786	1 retrocopy	retro_mmus_98,
Pongo abelii	ENSPPYG00000009536	3 retrocopies	retro_pabe_1489, retro_pabe_2226, retro_pabe_2814,
Pan troglodytes	ENSPTRG00000010451	3 retrocopies	retro_ptro_1170 , retro_ptro_1895, retro_ptro_2280,
Pteropus vampyrus	ENSPVAG00000008628	1 retrocopy	retro_pvam_1461,
Sarcophilus harrisii	ENSSHAG00000010974	1 retrocopy	retro_shar_753,
Sus scrofa	ENSSSCG00000023331	2 retrocopies	retro_sscr_544, retro_sscr_608,
Tursiops truncatus	ENSTTRG00000008535	1 retrocopy	retro_ttru_166,