RetrogeneDB ID: retro_opri_541

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_1637:168243..168792(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STRAP
• Ensembl ID: ENSOPRG00000015211
• Aliases: None
• Description: serine/threonine kinase receptor associated protein [Source:HGNC Symbol;Acc:30796]

Sequence

>retro_opri_541
CTTTGGGATCATGCTACTATGACAGAAGTGAAATCTCTAAATTTTAATATGTCTGTTAGTAGTATGGAGTATATTCCTGA
AGGAGAGATCTTGGTTATAACTTATGGACGATCTATTGCTTTTCATAGTGCAATAAGTTTGGACCCAATTAAATCCTTCG
AAGCTCCTGCAACTATCAATTCTGCATCTCTTCATCGTGAGAAAGAGTTTCTTGTTGCAGGTGATGAAGATTTTAAACTT
TATAAGTATGATTATAATAGTGGAGAAGAGTTAGAATCCTACAAAGGACACTTTGGTCCTATTCACTGTGTGAGATTTAG
TCCTGATGGAGAGCTTTATGCCAGTGGCTCTGAAGATGGAACACTGAGGCTGTGGCAAACTATAGTAGGAAAAACATACG
GCCTTTGGAAATGTGTGCTTCCTGAAGACGACAGTGGAGAGTTGGCCAAGCCCAAGATCAATTTCCCAGAGACAGCGGAA
GAGGAGCTAGAAGAAATTACCACGGAGAATTCAGATTCCATCTATTCTTCAACTCCTGAAGTTAAGGCT

Alignment

ORF - retro_opri_541 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.36 %
• Parental protein coverage: 52.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LWDHATMTEVKSLNFNMSVSSMEYIPEGEILVITYGRSIAFHSAVSLDPIKSFEAPATINSASLHREKEF
          LWDHATMTEVKSLNFNMSVSSMEYIPEGEILVITYGRSIAFHSA.SLDPIKSFEAPATINSASLHREKEF
Retrocopy LWDHATMTEVKSLNFNMSVSSMEYIPEGEILVITYGRSIAFHSAISLDPIKSFEAPATINSASLHREKEF

Parental  LVAGGEDFKLYKYDYNSGEELESYKGHFGPIHCVRFSPDGELYASGSEDGTLRLWQTVVGKTYGLWKCVL
          LVAG.EDFKLYKYDYNSGEELESYKGHFGPIHCVRFSPDGELYASGSEDGTLRLWQT.VGKTYGLWKCVL
Retrocopy LVAGDEDFKLYKYDYNSGEELESYKGHFGPIHCVRFSPDGELYASGSEDGTLRLWQTIVGKTYGLWKCVL

Parental  PEDDSGELAKPKINFPETAEEELEEITTENSDSIYSSTPEVKA
          PEDDSGELAKPKINFPETAEEELEEITTENSDSIYSSTPEVKA
Retrocopy PEDDSGELAKPKINFPETAEEELEEITTENSDSIYSSTPEVKA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_541 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007422	2 retrocopies	retro_chof_1098, retro_chof_1620,
Callithrix jacchus	ENSCJAG00000021593	1 retrocopy	retro_cjac_2503,
Homo sapiens	ENSG00000023734	2 retrocopies	retro_hsap_2092, retro_hsap_3723,
Gorilla gorilla	ENSGGOG00000009939	1 retrocopy	retro_ggor_1633,
Macaca mulatta	ENSMMUG00000013307	2 retrocopies	retro_mmul_1695, retro_mmul_985,
Mus musculus	ENSMUSG00000030224	1 retrocopy	retro_mmus_794,
Nomascus leucogenys	ENSNLEG00000004160	2 retrocopies	retro_nleu_1301, retro_nleu_1970,
Ochotona princeps	ENSOPRG00000015211	3 retrocopies	retro_opri_1029, retro_opri_217, retro_opri_541 ,
Pongo abelii	ENSPPYG00000004334	3 retrocopies	retro_pabe_2005, retro_pabe_3134, retro_pabe_3212,
Pan troglodytes	ENSPTRG00000004734	2 retrocopies	retro_ptro_1538, retro_ptro_2616,
Tursiops truncatus	ENSTTRG00000003466	2 retrocopies	retro_ttru_581, retro_ttru_974,