RetrogeneDB ID: retro_opri_1046

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6168:824..1924(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR24
• Ensembl ID: ENSOPRG00000012093
• Aliases: None
• Description: WD repeat domain 24 [Source:HGNC Symbol;Acc:20852]

Sequence

>retro_opri_1046
AGTGCCCTCAGCGTCTTTGAGATAGAGCCTGCAGCCGGTGGCATGCACTGGTTCTTGGACACGGCCGAGCGCTATGCTCT
GGCTGTCCGGCTGCTGGCCGAGCTCTGTGACCACAATGCCAAGGTGGCGTGGAAGCTAGGTCGCAACCAGGTGGCGCAGA
CGTGGACTATGCTGCGGATCATCTACTGCAGCCCGGGCCGGTATCCGCCGCCAGCGTCAACCACAGCGCGGACAAGAGCA
GCACCTGTGGCCTGCCACTCCTGAACAGTTTCAATCTGAAAGATGTGGACCCGGGGCTGGGCAGCGAGACACGACTGGAC
CGCAGCAAGGGAGATGCCCGGAGTGACACAGCCCTGCTTGACTCCTCAGCCACACTGCTCACCAATGAGGACAACGAGGA
GACGGAGGGCAGCGATGTGCCGGCCGACTATCTGCTGGGTGATGCTGAGGGCGACGAGGAGGAGCTGTACTTGCTGGACA
CCGAACACGCGCACCCTGAGGACCCCGAGTACGTGCTGCCGCAGGAGGCCTTCCCAGTGCGCCACGAGATTGTGGACACG
CCGCCGGGGCCAGAGCAGCTGCAGGACAAGGCTGAGTCCCCACACTTGAGTGGCAGCGAGGCGGACGCGGCCTCCCTGGC
CCCTGCAGACACTTTCTCGCTGCTCTCTGTGTCCCACGCGCTGTACGACAGCCAGCTGCCCTCCGACTTCTTTGGGGTGC
TGGTGCGGGACATGCTGCACTTCTACGCGGAGAGGGGCGACGTGCAGATGGTCGTGTCCGTGCTCATTGTGCTGGGCGAG
GACGTGCGCAAAGACATCGACGAGCAGACACAGGAGCACTGGTACACATCCTGCGTGGACCTGCTGCAGCGCTTCCGGCT
CTGGAACGTGTCCAACAAGGTGGTCAAGCTGAGCACCAGCCGGGCGATCAGCTGCCTCAACCAGGCCTCCACCACGCTGC
ACGTCAACTGCAGCCACTGCAAGCGACCCATGAGCAGCCACGGCTGGGTCTGTGACAGGTGCCACCGTCTGCCACCACGT
GGTCAAGGGCCTGTTCGTATGGTGCCAGGGCTGCAGCCATGGCGGCCACTTGCAGCACAT

Alignment

ORF - retro_opri_1046 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.51 %
• Parental protein coverage: 58.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SALSVFETEPAAGGMHWFVDTAERYALAGRPLAELCDHNAKVARELGRNQVAQTWTMLRVIYCSPGL-VS
          SALSVFE.EPAAGGMHWF.DTAERYALA.R.LAELCDHNAKVA..LGRNQVAQTWTMLR.IYCSPG..VS
Retrocopy SALSVFEIEPAAGGMHWFLDTAERYALAVRLLAELCDHNAKVAWKLGRNQVAQTWTMLRIIYCSPGR<VS

Parental  AAGVNHSAGKSSTCGLPLLNSFNLKDVAPGLGSETRLDRSKGDARSDTALLDSSATLLTNEDNEETEGSD
          AA.VNHSA.KSSTCGLPLLNSFNLKDV.PGLGSETRLDRSKGDARSDTALLDSSATLLTNEDNEETEGSD
Retrocopy AASVNHSADKSSTCGLPLLNSFNLKDVDPGLGSETRLDRSKGDARSDTALLDSSATLLTNEDNEETEGSD

Parental  VPADYLLGDAEGDEEXXXXXXXXXXXXEDPEYVL-QEA-PLR-EIVDTPPGPEQLQDKAESPHVSGSEAD
          VPADYLLGDAEGDEE............EDPEYVL.QEA.P.R.EIVDTPPGPEQLQDKAESPH.SGSEAD
Retrocopy VPADYLLGDAEGDEEELYLLDTEHAHPEDPEYVLPQEAFPVRHEIVDTPPGPEQLQDKAESPHLSGSEAD

Parental  AASLAPADTFSLLSVSHTLYDSRLPPDFFGVLVRDMLHFYAEGGDVQMAVSVLIVLGERVRKDIDEQTQE
          AASLAPADTFSLLSVSH.LYDS.LP.DFFGVLVRDMLHFYAE.GDVQM.VSVLIVLGE.VRKDIDEQTQE
Retrocopy AASLAPADTFSLLSVSHALYDSQLPSDFFGVLVRDMLHFYAERGDVQMVVSVLIVLGEDVRKDIDEQTQE

Parental  HWYTSYVDLLQRFRLWNVSNEVVKLSTSRAISCLNQASTTLHVNCSHCKRPMSSRGWVCDRCHRCASTCA
          HWYTS.VDLLQRFRLWNVSN.VVKLSTSRAISCLNQASTTLHVNCSHCKRPMSS.GWVCDRCHR......
Retrocopy HWYTSCVDLLQRFRLWNVSNKVVKLSTSRAISCLNQASTTLHVNCSHCKRPMSSHGWVCDRCHRLPPRGQ

Parental  VCHHVVKGLFVWCQGCSH
          .....V.GL..W.....H
Retrocopy GPVRMVPGLQPWRPLAAH

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_1046 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ochotona princeps	ENSOPRG00000012093	1 retrocopy	retro_opri_1046 ,