RetrogeneDB ID: retro_opri_960

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5035:116284..117585(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKIL
• Ensembl ID: ENSOPRG00000015606
• Aliases: None
• Description: SKI-like oncogene [Source:HGNC Symbol;Acc:10897]

Sequence

>retro_opri_960
TCATCATGCCCAGTAAATGAAACTAGCAGTGCCTTTGAAGTGGACCATGAATGCTTGGGCAAATGTCAGGGCCTGTTTGC
ACTCAGTTCTATGTGCAGTCTGACGCTCCGTTTATTCAGTGTCTGGAGTGCTGTGGGATGTTTGCACCTCAAACGTTTGT
GATGCATTCTCACAGATCACCTGACAAAAGAACTTGCCACTGGGGTTTTGAATCAGCCAAATGGCACTGTTATCTTCATG
TGAACCAAAAGTACTTGGGGACACCTGAAGAAAAGAAGCTGAAAATAATTTTAGAAGAAATGAAGGAGAAATTTAGCATG
AGAAATGGGAAGAGAACTCAACCTAAGGCAGATGCGCCATCAGGAATGGAATTACAGTCATGGTATCCTGTTATAAAGCA
GGAAGGTGACCATGTTTCTCCGACACATTCATTTCTACATCCCAGCTACTATTTACACATGTGTGATAAAGTGGTTGCCC
CCAATGTGTCGCTTACTTCTGCTGTATCCCAGTCCAAAGAGGTTACAAAGACAGAGGCAAGTAAGACTGTATCACGACTG
CCAGAGAAACAGCACGCTGGTGGGAAACCTCAAAAAATAGCGTCTTATCCGGATGTCTCACTTGAGGAACAGGAGAAGAT
GGATTTGAAAATAAACAGAGAATTATATGGTCGTTCAGATCGATCAATCTTAAATAGTTCTCCGAATAAGAAGAAATCTG
ACTCTGCCACTTGCAACTTAGTCAGAGACACAAGCAATGTGGGAGTTGACCGTGATGCTACAGCCTCATTCCTGCTTCTT
GTCAAAGATGTCACTTGTGAAGATGATAAAGGAAAAATCATGGAAGAAGTAATGAGAACTTATGTAAAACAACAGGACAA
ACTGAACTCAATTTTGCAAAAAAAAGCAACAACTTCAGATGGAAGTGGAAATGTTGAGTAGTTCAAAAGCGATGAGGGAA
CTCACTGAAGAACAGCAGAATCTGCAGAAGGTACTTGAGTCTTTACAGAGTGAACATGCTCAGAGAATGGAAGAGTTCTA
TGTTGAGCAGAAGGACTTAGAGAAAAAATTAGAGCAGGTAATGAAGCAGAAATGTACCTGTGACTCAAATTTAGAGAAAG
ACAAGAGGCCGAATATGCAGCACAGTTGGCGGAACTGAGACAGCGACTGGACCTTGCTGAGGCTGATAGGCAAGAACTCC
AAGACGAACTCAGACAGGAGCGGGAGGCAAGACAGAAGTTAGAGATGATGATCAAAGAGCTGAAGCTGCAAATTTTGAAA
TCATCGAAGGCTGCTAAAGAA

Alignment

ORF - retro_opri_960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.51 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLAQLKETGSAFEVEHECLGKCQGLFA-PQFYVQPDAPCIQCLECCGMFAPQTFVMHSHRSPDKRTCHWG
          S.....ET.SAFEV.HECLGKCQGLFA..QFYVQ.DAP.IQCLECCGMFAPQTFVMHSHRSPDKRTCHWG
Retrocopy SSCPVNETSSAFEVDHECLGKCQGLFA<TQFYVQSDAPFIQCLECCGMFAPQTFVMHSHRSPDKRTCHWG

Parental  FESAKWHCYLHVNQKYLGTPEEKKLKIILEEMKEKFSMRNGKRTQPKADAPSGMELQSWYPVIKQEGDHV
          FESAKWHCYLHVNQKYLGTPEEKKLKIILEEMKEKFSMRNGKRTQPKADAPSGMELQSWYPVIKQEGDHV
Retrocopy FESAKWHCYLHVNQKYLGTPEEKKLKIILEEMKEKFSMRNGKRTQPKADAPSGMELQSWYPVIKQEGDHV

Parental  SPTHSFLHPSYYLYMCDKVVAPNVSLTSAVSQSKEVAKTEASKTASRLPEKQHAGGKPQKTASYPDVSLE
          SPTHSFLHPSYYL.MCDKVVAPNVSLTSAVSQSKEV.KTEASKT.SRLPEKQHAGGKPQK.ASYPDVSLE
Retrocopy SPTHSFLHPSYYLHMCDKVVAPNVSLTSAVSQSKEVTKTEASKTVSRLPEKQHAGGKPQKIASYPDVSLE

Parental  EQEKMDLKINRELYGRSDRSILNSSPNKKKSDPATCNLVRDTSNVGVDRDATASSLLLVKDVTCEDDKGK
          EQEKMDLKINRELYGRSDRSILNSSPNKKKSD.ATCNLVRDTSNVGVDRDATAS.LLLVKDVTCEDDKGK
Retrocopy EQEKMDLKINRELYGRSDRSILNSSPNKKKSDSATCNLVRDTSNVGVDRDATASFLLLVKDVTCEDDKGK

Parental  IMEEVMRTYVKQQEKLNSIL-QKKQQLQMEVEMLSSSKAMRELTEEQQNLQKELESLQSEHAQRMEEFYV
          IMEEVMRTYVKQQ.KLNSIL....QQLQMEVEMLSSSKAMRELTEEQQNLQK.LESLQSEHAQRMEEFYV
Retrocopy IMEEVMRTYVKQQDKLNSIL>XXXQQLQMEVEMLSSSKAMRELTEEQQNLQKVLESLQSEHAQRMEEFYV

Parental  EQKDLEKKLEQVMKQKCTCDSNLEKDK-EAEYAAQLAELRQRLDLAEADRQELQDELRQEREARQKLEMM
          EQKDLEKKLEQVMKQKCTCDSNLEKDK.EAEYAAQLAELRQRLDLAEADRQELQDELRQEREARQKLEMM
Retrocopy EQKDLEKKLEQVMKQKCTCDSNLEKDK<EAEYAAQLAELRQRLDLAEADRQELQDELRQEREARQKLEMM

Parental  IKELKLQILKSSKAAKE
          IKELKLQILKSSKAAKE
Retrocopy IKELKLQILKSSKAAKE

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_960 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008923	1 retrocopy	retro_dnov_1589,
Ochotona princeps	ENSOPRG00000015606	1 retrocopy	retro_opri_960 ,