RetrogeneDB ID: retro_opri_1106

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_718:47576..48289(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBB
• Ensembl ID: ENSOPRG00000014770
• Aliases: None
• Description: tubulin, beta class I [Source:HGNC Symbol;Acc:20778]

Sequence

>retro_opri_1106
ATGAGGGAGATTGTGCACATCCAGGCCGGCCAGTGCGGCAACCAGATCGGTGCCAAGTTCTAGGAGGTGATGAGCGATGA
GCACGGCATCGACCCCACCGGCACCTACCGCGGCGACAGCGACCTGTAGCTCGACCGCCATCTCCGTGTACTACAGTGAA
GCCGCAGGTGGCAAATACGTTCCTCGTGCTATCTTGGTGGACTTAGAACCTGGGACCATGGACTCTGTTCGCTCAGGTCC
TTTTGGTCAGATCTTCAGACCAGACAACTTTGGTTTTGGTCAGTCCGGGGCAGGCAACAACTGGGCCAAGGGCCACTACA
CAGAGGGGGCCGAGCTGGGCGACTCAGTGCTCGATGTGGTGCGGAAGGAGGCCGAGAGCTGTGACTGCCTTCAGGGCTTC
CAGCTGACCCACTCGCTCGGTGGGGGGCACCGGCTCAGGCATGGGCACCCTGCTCATCAGCAAGATCCGAGAAGAGTATC
CCGATCGCATCATGAACACCTTCAGCGTGGTGCCCTCGCCCAAGGTGTCCGACACTGTCGTGGAGCCCTACAACGCCACG
CTGTCTGTGCACCAGCTGCTGGAGAACACGGATGAGACCTATTGCATTGACAACGAGGCCCTCTTCGACTTCTGCTTCCG
CACCCTTAAGCTGACCACGCCCACCTATGGCGACCTCAACCACCTGGTGTCTGCCACCATGAGCGGGGTCACC

Alignment

ORF - retro_opri_1106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.56 %
• Parental protein coverage: 53.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDR-ISVYYNEATGGKYVPRAILVDLE
          MREIVHIQAGQCGNQIGAKF.EV.SDEHGIDPTGTY.GDSDL.LDR.ISVYY.EA.GGKYVPRAILVDLE
Retrocopy MREIVHIQAGQCGNQIGAKF*EVMSDEHGIDPTGTYRGDSDL*LDR>ISVYYSEAAGGKYVPRAILVDLE

Parental  PGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSL
          PGTMDSVRSGPFGQIFRPDNF.FGQSGAGNNWAKGHYTEGAEL.DSVLDVVRKEAESCDCLQGFQLTHSL
Retrocopy PGTMDSVRSGPFGQIFRPDNFGFGQSGAGNNWAKGHYTEGAELGDSVLDVVRKEAESCDCLQGFQLTHSL

Parental  G-GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALY
          G.GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQL.ENTDETYCIDNEAL.
Retrocopy G>GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLLENTDETYCIDNEALF

Parental  DICFRTLKLTTPTYGDLNHLVSATMSGVT
          D.CFRTLKLTTPTYGDLNHLVSATMSGVT
Retrocopy DFCFRTLKLTTPTYGDLNHLVSATMSGVT

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_1106 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 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013572	1 retrocopy	retro_etel_641,
Gorilla gorilla	ENSGGOG00000022655	4 retrocopies	retro_ggor_2388, retro_ggor_244, retro_ggor_2519, retro_ggor_2651,
Macropus eugenii	ENSMEUG00000015992	1 retrocopy	retro_meug_978,
Macaca mulatta	ENSMMUG00000023684	2 retrocopies	retro_mmul_2501, retro_mmul_375,
Nomascus leucogenys	ENSNLEG00000005348	1 retrocopy	retro_nleu_498,
Otolemur garnettii	ENSOGAG00000032213	1 retrocopy	retro_ogar_2391,
Ochotona princeps	ENSOPRG00000014770	4 retrocopies	retro_opri_1106 , retro_opri_237, retro_opri_46, retro_opri_656,
Pongo abelii	ENSPPYG00000016419	4 retrocopies	retro_pabe_2920, retro_pabe_3210, retro_pabe_3698, retro_pabe_467,
Pan troglodytes	ENSPTRG00000017939	3 retrocopies	retro_ptro_151, retro_ptro_2527, retro_ptro_2677,