RetrogeneDB ID: retro_ptro_1940

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:160549660..160550119(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040050
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000005076
• Aliases: None
• Description: None

Sequence

>retro_ptro_1940
GGGGTACTTTGGTCCTTGGTGGAAGCATCTAGCTCAGGTGTGTCGGTACTGAGCCTGTGTGAGAAAGGTGATGCCGTGAT
TATGGAAGAAACAGGGAAAATCTTCAAGAAAGAAAAGGAAATGAAGAAAGGTATTGCTTTTCCCACCAGCATTTCAGTAA
ATAACTGTGTATGTCACTTCTCCCCTTTGAAGAGCAACCAGGATTATATTCTCAAGGAAGGTGACTTGGTAAAAATTGAA
CTTGGGGTCCATGTGGATGGCTTCATCGCTAATGTAGCTCATACTTTTGTGGTTGATGTAGCTCAGGGGACCCAAGTAAC
AGGGAGGAAGGCAGATGTTATTAAGGCAGCTCACCTTTGTGCTGAAGCTGCCCTACGCCTGGTCAAACCTGGAAATCAGA
ACACACAAGTGACACAAGCCTGGAACAAAGTTGCCCACTCATTTAACTGCACGCCAATA

Alignment

ORF - retro_ptro_1940 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.73 %
• Parental protein coverage: 73.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKKEKEMKKGIAFPTSISVNNCVCHFSPLKSDQDYI
          GVL.SLVEASSSGVSVLSLCEKGDA.IMEETGKIFKKEKEMKKGIAFPTSISVNNCVCHFSPLKS.QDYI
Retrocopy GVLWSLVEASSSGVSVLSLCEKGDAVIMEETGKIFKKEKEMKKGIAFPTSISVNNCVCHFSPLKSNQDYI

Parental  LKEGDLVKIDLGVHVDGFIANVAHTFVVDVAQGTQVTGRKADVIKAAHLCAEAALRLVKPGNQNTQVTEA
          LKEGDLVKI.LGVHVDGFIANVAHTFVVDVAQGTQVTGRKADVIKAAHLCAEAALRLVKPGNQNTQVT.A
Retrocopy LKEGDLVKIELGVHVDGFIANVAHTFVVDVAQGTQVTGRKADVIKAAHLCAEAALRLVKPGNQNTQVTQA

Parental  WNKVAHSFNCTPI
          WNKVAHSFNCTPI
Retrocopy WNKVAHSFNCTPI

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	1.20 RPM	39.27 RPM
SRP007412_cerebellum	1.43 RPM	26.49 RPM
SRP007412_heart	0.73 RPM	18.10 RPM
SRP007412_kidney	0.97 RPM	109.58 RPM
SRP007412_liver	0.65 RPM	75.35 RPM
SRP007412_testis	4.22 RPM	75.03 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1940 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1940 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Callithrix jacchus	ENSCJAG00000011811	2 retrocopies	retro_cjac_4214, retro_cjac_4215,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Pan troglodytes	ENSPTRG00000005076	6 retrocopies	retro_ptro_1289, retro_ptro_1389, retro_ptro_1940 , retro_ptro_2471, retro_ptro_2846, retro_ptro_3263,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,