RetrogeneDB ID: retro_opri_637

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_21045:12493..13174(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT21
• Ensembl ID: ENSOPRG00000006689
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 21 [Source:HGNC Symbol;Acc:13870]

Sequence

>retro_opri_637
ATGTCTGTGGTACCGCCCAATCGCTCGCAGACCGGCTGGCCCCGAGGGGTCAACCAGTTCGGCAACAAGTACATCCGGCA
GACCAAGCCCCTCACCCTGGAGCGCACCATCAACCTTTACCGACTTACCAATTACGCTTTTGGGACCAAAGAGCCTGTCT
ATGAGAAGGACAGTTCCGTCGCAGCCAGATTTCAGCGCATGAGGGAAGAATTCGATAAGATTGGAATGAGGAGGACTGTG
GAAGGGGTTCTGATTGTACACGAGCACCGACTACCACACGTGCTACTGCTGCAGCTGGGAACAACTTTCTTCAAATTGCC
TGGTGGTGAACTTAATCCAGGAGAAGATGAAGTTGAAGGACTAAAACGCTTAATGACAGAGATACTAGGCCGTCAAGATG
GAGTCCTGCAAGACTGGGTCATTGATGACTGCATTGGTAACTGGTGGAGACTGAATTTTGAACCTCCGCAGTACCCATAT
ATTCCTGCACATGTTACAAAGCCTAAGGAGCATAAGAAGTTGTTTCTGGTTCAACTTCAAGAGAAAGCCTTGTTTGCAGT
CCCTAAAAATTACAAGCTGGTAGCTGCACCTTTGTTTGAATTGTATGACAATGCACCAGGATATGGACCCATCATTTCTA
GTCTTCCTCAACTGTTGAGCAGGTTCAATTTTATATACAAC

Alignment

ORF - retro_opri_637 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVVPPNRSQTGWPRGVNQFGNKYIQQTKPLTLERTINLYPLTNTL--DKEPLYEKDSSVAARFQRMREE
          MSVVPPNRSQTGWPRGVNQFGNKYI.QTKPLTLERTINLY.LTN.....KEP.YEKDSSVAARFQRMREE
Retrocopy MSVVPPNRSQTGWPRGVNQFGNKYIRQTKPLTLERTINLYRLTNYAFGTKEPVYEKDSSVAARFQRMREE

Parental  FDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWV
          FDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWV
Retrocopy FDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWV

Parental  IDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGP
          IDDCIGNWWR.NFEPPQYPYIPAH.TKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGP
Retrocopy IDDCIGNWWRLNFEPPQYPYIPAHVTKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGP

Parental  IISSLPQLLSRFNFIYN
          IISSLPQLLSRFNFIYN
Retrocopy IISSLPQLLSRFNFIYN

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_637 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Cavia porcellus	ENSCPOG00000003705	1 retrocopy	retro_cpor_1054,
Felis catus	ENSFCAG00000008669	1 retrocopy	retro_fcat_1843,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Mus musculus	ENSMUSG00000031754	3 retrocopies	retro_mmus_1949, retro_mmus_1950, retro_mmus_2142,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Otolemur garnettii	ENSOGAG00000014888	2 retrocopies	retro_ogar_1450, retro_ogar_630,
Ochotona princeps	ENSOPRG00000006689	1 retrocopy	retro_opri_637 ,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tursiops truncatus	ENSTTRG00000013545	1 retrocopy	retro_ttru_1087,