RetrogeneDB ID: retro_opri_24

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_1059:57994..58888(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2B
• Ensembl ID: ENSOPRG00000007990
• Aliases: None
• Description: transformer 2 beta homolog (Drosophila) [Source:HGNC Symbol;Acc:10781]

Sequence

>retro_opri_24
CAGCTTCGACGGAGGGCCAGCGAGCGGCGACAGCAGCCAGGCGTCATGAGCGACAGCGGCGAGCAGAACTACGGCGAGCA
GGGATCCCGCTCTGCTTCCCGAAGTGGAAGTGCTCACAGATCGGGGAATTCTGCAAGGCATAGCCCTGCAAGGTCTCACT
CCAAGGAAGATTCCAGGCGTTCCAGATCCAAGTCCAGGTCCAGATCCGAATCTAGGTCTAGATCCAGAAGAAGCTCGCGG
AAGCGTTACACGAGGTCGCGGTCCCGGTCCCGGTCCCATAGACGATCCCGTAGCAGGTCATACAGTCGCGATTATCGCAG
ACGGCATAGCCACAGCCATTCTCCCATGTCCACTCGTAGGCGCCACGTTGGGAACCAGGCAAACCCTGACCCCAACCGCT
GTCTTGGAGTATTTGGTTTGAGCTTGTACACCACAGAGAGAGATCTCAGAGAAGTGTTTTCTAAGTACGGGCCCATTGCC
GACGTGGCTGTCGTGTATGACCAGCAGTCGCGGCGCTCCCGAGGATTTGCCTTTGTTTATTTTGAGAGCGTAGATGATGC
CAAGGAAGCTAAGGAGCGCACCAATGGGATGGAGCTGGATGGGCGCAGGATCAGAGTTGATTTCTCTATAACAAAAAGAC
CACATACTCCAACACCAGGAATTTACATGGGGAGGCCCACGTATGGCAGTTCACGCCGTCGGGATTATTACGACCGAGGG
TATGACCGAGGCTATGACGACCGAGACTACTATAGCAGGCCGTATAGAGGGGGTGGCTGGAGAGCCGCCCAGGAGAGAGA
GGAGATCTATAGAAGACGCTCGCCTTCACCCTACTATAGTCGTGGCGGATACAGATCGCGCTCCAGGTCGCGCTCCTACT
CCCCCCGCCGCTAC

Alignment

ORF - retro_opri_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.54 %
• Parental protein coverage: 94.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLRRKRGGR-QQPGVMSDSGEQNYGERESRSASRSGSAHGSGKSARHTPARSRSKEDSRRSRSKSRSRSE
          QLRR....R.QQPGVMSDSGEQNYGE..SRSASRSGSAH.SG.SARH.PARS.SKEDSRR..........
Retrocopy QLRRRASERRQQPGVMSDSGEQNYGEQGSRSASRSGSAHRSGNSARHSPARSHSKEDSRRXXXXXXXXXX

Parental  SRSRSRRSSRRHYTRSRSRSRSHRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGL
          ......RSSR..YT.........RRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGN.ANPDPN.CLGVFGL
Retrocopy XXXXXXRSSRKRYTXXXXXXXXXRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNQANPDPNRCLGVFGL

Parental  SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI
          SLYTTERDLREVFSKYGPIADV..VYDQQSRRSRGFAFVYFE.VDDAKEAKER.NGMELDGRRIRVDFSI
Retrocopy SLYTTERDLREVFSKYGPIADVAVVYDQQSRRSRGFAFVYFESVDDAKEAKERTNGMELDGRRIRVDFSI

Parental  TKRPHTPTPGIYMGRPTYGSSRRRDYYDRGYDRGYDDRDYYSRSYRGGGGGGGGWRAAQDRDQIYRRRSP
          TKRPHTPTPGIYMGRPTYGSSRRRDY....YDRGYD.R.Y..R.Y......GGGWRAAQ.R..IYRRRSP
Retrocopy TKRPHTPTPGIYMGRPTYGSSRRRDY----YDRGYD-RGYDDRDYYSRPYRGGGWRAAQEREEIYRRRSP

Parental  SPYYSRGGYRSRSRSRSYSPRRY
          SPYYSRGGYRSRSRSRSYSPRRY
Retrocopy SPYYSRGGYRSRSRSRSYSPRRY

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_24 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.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001697	2 retrocopies	retro_btau_1245, retro_btau_850,
Myotis lucifugus	ENSMLUG00000005781	2 retrocopies	retro_mluc_2565, retro_mluc_2567,
Mustela putorius furo	ENSMPUG00000003157	1 retrocopy	retro_mputfur_673,
Mus musculus	ENSMUSG00000022858	6 retrocopies	retro_mmus_1187, retro_mmus_2253, retro_mmus_2313, retro_mmus_3139, retro_mmus_3617, retro_mmus_756,
Ochotona princeps	ENSOPRG00000007990	2 retrocopies	retro_opri_24 , retro_opri_930,
Ochotona princeps	ENSOPRG00000016593	1 retrocopy	retro_opri_372,
Rattus norvegicus	ENSRNOG00000001783	4 retrocopies	retro_rnor_1130, retro_rnor_1915, retro_rnor_2156, retro_rnor_2807,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,