RetrogeneDB ID: retro_opri_680

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_237:186852..188349(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBAP1
• Ensembl ID: ENSOPRG00000009100
• Aliases: None
• Description: ubiquitin associated protein 1 [Source:HGNC Symbol;Acc:12461]

Sequence

>retro_opri_680
ATGGCTTCTAAGAAGTTGGGTGCAGATAGTCATGGGACTTTCAGTTACCTTGATGATGTCCCATTGAAGATAGGAGACAA
ATTCAAAACACCAGCTAAAGTTGGTCTACCTATTGGCTTCTCCTTGCCTGACTGTTTGCAGGTTGTCAGAGAAGTACAGT
ATGACTTCTCCTTGGAAAAGAAGACCATCGAGTGGGCCGAGGACGTCGGGAAGATCCAGGACGCCCAGCGGGAAGCAGAA
CGCAAGGCTCAGGAGGCGGAACCCAAAGTCAATTCCAAGAGTGGCCCAGAGGGCGATAACAAAATGAGCTTCTCCAAGAC
TCAAAGTACAGCCACAATGCCACCTCCTATTAACCCCATCCTTGCCAGCCTGCAGCACAACAGCATCCTCACTCCAACCC
GGGTCAGCAGTAGTGCCACGAAGCAAAAAGCCCTCAGCCCCCCACACACAAAGGCAGATTTCAATCCTGCCGACTTTGAG
TGTGAAGAGGACCCATTTGATAATCTGGAGTTAAAAACCACTGATGAGAAAGAAGAGCTGAGAAACATTCTGGTGGGAGC
CACGGGACCCATTATGGCTCAGTTATTGGACAGTAACTTGCCCAGAGGCGGCTCCGGGTCAGTGTTACAGGATGAGGAGG
TCCTGGCATCCTTGGAGCGGGCAACCCTGGATTTCAAGCCTCTTCACAAACCCAATGGCTTTATAACCTTACCACAGTTG
GGCAACTGTGAAAGATGTCGCTGTCTTCCAAAGTGTCCCTCCCCCCCGATTCCTGCAGTAAGCAATATCAAATCCCTGTC
CTTCCCCAAACTTGACTCTGATGACAGCAATCAGAAGACAGCCAAACTGGCAAGCACTTTCCATAGCACATCCTGCCTCT
GCAGTGGTACGCTACTGAACTCCTTCAAGCCTTCCACCCAAAGCAGTGCCAGTGAGCTCAAAGGGCATCATACTCTTGGG
CTTTCAGCTTTGAACTTGGACAGTTGCACTGAGGTGCCCACCCTTGCACCCTCCCAGACGCCTTCCCACTCAGTCTCGTC
TGTGTGCACAGAAGAGTCATCACCTCCACAGGCAGGCTCCGCGGTCGCCCCTCCTAATTTCTCAATGTCACAAGTGCCCA
GGTGCCCCCAGGCCTACTCTGAGCTACAGACATTGTCCCCCAGTGAGCGGCAATGTGTGGAGACAGTGGTCAACATGGGC
TACTCCTACGATTGTGTCCTGAGAGCTATGAAGAAGAAAGGAGAGACTATTGAGCAGATCCTCTACTATCTCTTTGCACA
TGGACAACTGTGTGAGAAGGGCTTTGACCCTCTGTTGGTGGAAGAGGCTTTGGAAATGCACCAGTGTTCAGAAGAAAAGA
AGATGGAGTTTCTTCAGTTAATGAGCAAATTTAAGGAAATGGGCTTTGAACTGAAGGACATTAAGGAAGCGTTGGTATTA
CACAACAATGACCAGGACAATGCTTTGGAAGACCTCATGGCCCGGGCAGGAGCCAGC

Alignment

ORF - retro_opri_680 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASKKLGADSHGTFSYLDDVPFKIGDKFKTPAKVGLPIGFSLPDCLQVVREVQYDFSLEKKTIEWAEDVR
          MASKKLGADSHGTFSYLDDVP.KIGDKFKTPAKVGLPIGFSLPDCLQVVREVQYDFSLEKKTIEWAEDV.
Retrocopy MASKKLGADSHGTFSYLDDVPLKIGDKFKTPAKVGLPIGFSLPDCLQVVREVQYDFSLEKKTIEWAEDVG

Parental  KIQDAQREAERKAQEAEAKVNSKSGPEGDNKMSFSKTQSIATMPPPINPILASLQHNSILTPTRVSSSAT
          KIQDAQREAERKAQEAE.KVNSKSGPEGDNKMSFSKTQS.ATMPPPINPILASLQHNSILTPTRVSSSAT
Retrocopy KIQDAQREAERKAQEAEPKVNSKSGPEGDNKMSFSKTQSTATMPPPINPILASLQHNSILTPTRVSSSAT

Parental  KQKALSPPHTKADFNPADFECEEDPFDNLELKTIDEKEELRNILVGATGPIMAQLLDSNLPRGGSGSVLQ
          KQKALSPPHTKADFNPADFECEEDPFDNLELKT.DEKEELRNILVGATGPIMAQLLDSNLPRGGSGSVLQ
Retrocopy KQKALSPPHTKADFNPADFECEEDPFDNLELKTTDEKEELRNILVGATGPIMAQLLDSNLPRGGSGSVLQ

Parental  DEEVLASLERATLDFKPLHKPNGFITLPQLGNCE-KMSLSSKVSL-PPIPAVSNIKSLSFPKLDSDDSNQ
          DEEVLASLERATLDFKPLHKPNGFITLPQLGNCE.KMSLSSKVSL.PPIPAVSNIKSLSFPKLDSDDSNQ
Retrocopy DEEVLASLERATLDFKPLHKPNGFITLPQLGNCE<KMSLSSKVSL>PPIPAVSNIKSLSFPKLDSDDSNQ

Parental  KTAKLASTFHSTSCLRSGTLLNSFKPSTQSSASELNGHHTLGLSALNLDSGTEVPTLAPSQTPSHSVLSV
          KTAKLASTFHSTSCL.SGTLLNSFKPSTQSSASEL.GHHTLGLSALNLDS.TEVPTLAPSQTPSHSV.SV
Retrocopy KTAKLASTFHSTSCLCSGTLLNSFKPSTQSSASELKGHHTLGLSALNLDSCTEVPTLAPSQTPSHSVSSV

Parental  CTEESSPPQAGSAVAPPNFSMSQVPSCPQAYSELQTLSPSERQCVETVVNMGYSYDCVLRAMKKKGENIE
          CTEESSPPQAGSAVAPPNFSMSQVP.CPQAYSELQTLSPSERQCVETVVNMGYSYDCVLRAMKKKGE.IE
Retrocopy CTEESSPPQAGSAVAPPNFSMSQVPRCPQAYSELQTLSPSERQCVETVVNMGYSYDCVLRAMKKKGETIE

Parental  QILDYLFAHGQLCEKGFDPLLVEEALEMHQCSEEKMMEFLQLMSKFKEMGFELKDIKEALVLHNNDQDNA
          QIL.YLFAHGQLCEKGFDPLLVEEALEMHQCSEEK.MEFLQLMSKFKEMGFELKDIKEALVLHNNDQDNA
Retrocopy QILYYLFAHGQLCEKGFDPLLVEEALEMHQCSEEKKMEFLQLMSKFKEMGFELKDIKEALVLHNNDQDNA

Parental  LEDLMARAGAS
          LEDLMARAGAS
Retrocopy LEDLMARAGAS

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_680 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000011672	1 retrocopy	retro_eeur_466,
Myotis lucifugus	ENSMLUG00000013063	1 retrocopy	retro_mluc_2305,
Otolemur garnettii	ENSOGAG00000015802	1 retrocopy	retro_ogar_557,
Ochotona princeps	ENSOPRG00000009100	3 retrocopies	retro_opri_355, retro_opri_477, retro_opri_680 ,
Ictidomys tridecemlineatus	ENSSTOG00000028294	1 retrocopy	retro_itri_1318,
Tarsius syrichta	ENSTSYG00000013035	2 retrocopies	retro_tsyr_1908, retro_tsyr_846,