RetrogeneDB ID: retro_opri_1039

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_6116:5947..7641(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX18
• Ensembl ID: ENSOPRG00000001701
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 [Source:HGNC Symbol;Acc:2741]

Sequence

>retro_opri_1039
TTGTCGGAGGCGCAAAATGGAGCCATGACTGAAGACGTGGTGGAAAAGATCAAAGTTAAACAATCCCCCCAGAAACCCGC
AGCACTAACCAACGGAGAAATGGCAGCAGAGTCGCCCAGTCCCAAATCGAATAAGAAAAAGAAGAAATGTGCCACACCAA
CCAATGGCGAAGCGGCAACAGAGTTGCCCAATCCCGAATCAAGGAAGAAGAAAAAGAAGAAAAAGAGAAAGCTGGCGAAT
GATGCTGGGCCTGATGCAAAAAAAGCAAAAGTTGAAGGCAGCGACACCGAGGCCCCTAAAGAAACGGAATCCAGTGTGGC
GGCGGCAAACAACAAGGAGGACAGTGAAGTCCCCAGCCTGCCCCTGGGACTGACAGGAGCTTTTGAGGATACTTCCTTTG
AATCTCTAAGTAATCTCGTCAATGAAAACACTCTGAAGGCAATAAAAGAAATGGGCTTCACAAACCTGACTGAAATTCAA
CATAAAAGTGTCAGACCCCTTCTGGAAGGCAGAGATCTTCTAGCAGCTGCAAAGACAGGGAGCGGCAAAACCCTGGCATT
TCTCATCCCTGCGGTTGAACTGATTGTGAAGTTAAAGTTCATGCCCAGGAACGGAACAGGAGTCCTGATTCTGTCCCCGA
CTAGAGAGCTGGCCATGCAGACATTTGGGGTTCTGAAGGAGCTGATGACCCACCATGTGCACACGTACGGCCTGATAATG
GGGGGCAGCAACAGGTCCGCCGAAGCACAGAAACTTGCCAACGGGATCAACATTGTGGCCACCCTGGCCGGCTGCTGGAC
CACATGCAGAACACCCCAGGGTTTATGTATAAGAACCTGCAGTGTTTGGTGATTGATGAGGCTGATCGCATCCTGGATGT
TGGATTTGAAGAGGAATTGAAGCAAATTATTAAACTTTTGCCAACCCGCAGGCAGACCATGCTCTTCTCTGCCACACAAA
CTCGGAAAGTGGAGGACCTGGCGAGGATTTCTCTGAAGAAGGAGCCGTTGTACGTCGGTGTCGATGACGACAAAGCCAAC
GCCACGGTGGACGGCCTCGAGCAGGGATATGTTGTTTGTCCCTCAGAAAAGAGATTCCTACTGCTCTTCACATTCCTTAA
GAAGAACCGAAAGAAGAAACTCATGGTCTTCTTCTCCTCCTGCATGTCCGTGAAATACCACTACGAGCTGCTGAACTACA
TCGACCTGCCCGTGCTGGCCATCCACGGAAAGCAGAAGCAGAACAAGCGGACAACCACGTTCTTCCAGTTCTGCAACGCA
GACTCGGGGATATTGCTGTGTACAGATGTGGCCGCAAGGGGGCTGGATATTCCTGAAGTGGACTGGATTGTCCAGTACAA
CCCTCCGGATGACCCTAAGGAATATATTCACTGTGTAGGTAGAACAGCCCGGGGTCTGAACGGACGAGGGCACGCTCTGC
TCATTTTGCGTCCAGAAGAACTGGGTTTCCTTCGTTACTTAAAGCAATCCAAGGTTCCATTAAGTGAATTCGACTTCTCC
TGGTCTAAAATCGCCAACATTCAGTCTCAGCTTGAGAAACTGATCGAGAAGAATTACTTCCTTCACAAGTCAGCCCAGGA
AGCCTATAAGTCATACATACGCGCTTATGATTCCCATTCTCTGAAGCAGATCTTCAATGTCAATAACTTAAATTTGCCTC
AGGTGGCACTGTCT

Alignment

ORF - retro_opri_1039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.66 %
• Parental protein coverage: 86.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSEDQNGDVPEEAMARGKPTKAPKPSMSAGLSEAQNGAPPEDVVEVKVKQSTQKPAALTNGEAATELPNP
          LSE.QNG...E......K......P...A.L....NG.........K......K.A..TNGEAATELPNP
Retrocopy LSEAQNGAMTEDVVEKIKVKQS--PQKPAALT---NGEMAAESPSPKSNKKKKKCATPTNGEAATELPNP

Parental  ESRKKKKKKKRKLVNDAGPDAKKAKVEGSDTEAPKEAASSVAAADNEEEDSEVPSLPLGLTGAFEDTSFE
          E...........L.NDAGPDAKKAKVEGSDTEAPKE..SSVAAA.N.E.DSEVPSLPLGLTGAFEDTSFE
Retrocopy EXXXXXXXXXXXLANDAGPDAKKAKVEGSDTEAPKETESSVAAANNKE-DSEVPSLPLGLTGAFEDTSFE

Parental  SLSNLVNENTLKAIKEMGFTNMTEIQHKSVRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMPRN
          SLSNLVNENTLKAIKEMGFTN.TEIQHKSVRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMPRN
Retrocopy SLSNLVNENTLKAIKEMGFTNLTEIQHKSVRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLKFMPRN

Parental  GTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGINIIVAT-PGRLLDHMQNT
          GTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGINI.VAT.PGRLLDHMQNT
Retrocopy GTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLANGINI-VAT<PGRLLDHMQNT

Parental  PGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVD
          PGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVD
Retrocopy PGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYVGVD

Parental  DDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQ
          DDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQ
Retrocopy DDKANATVDGLEQGYVVCPSEKRFLLLFTFLKKNRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQ

Parental  KQNKRTTTFFQFCNADSGILLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTARGLNGRGHALLI
          KQNKRTTTFFQFCNADSGILLCTDVAARGLDIPEVDWIVQY.PPDDPKEYIH.VGRTARGLNGRGHALLI
Retrocopy KQNKRTTTFFQFCNADSGILLCTDVAARGLDIPEVDWIVQYNPPDDPKEYIHCVGRTARGLNGRGHALLI

Parental  LRPEELGFLRYLKQSKVPLSEFDFSWSKISNIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIF
          LRPEELGFLRYLKQSKVPLSEFDFSWSKI.NIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIF
Retrocopy LRPEELGFLRYLKQSKVPLSEFDFSWSKIANIQSQLEKLIEKNYFLHKSAQEAYKSYIRAYDSHSLKQIF

Parental  NVNNLNLPQVALS
          NVNNLNLPQVALS
Retrocopy NVNNLNLPQVALS

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_1039 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004191	6 retrocopies	retro_chof_1221, retro_chof_1539, retro_chof_1636, retro_chof_2416, retro_chof_2418, retro_chof_721,
Callithrix jacchus	ENSCJAG00000021414	5 retrocopies	retro_cjac_2309, retro_cjac_2743, retro_cjac_4179, retro_cjac_644, retro_cjac_753,
Myotis lucifugus	ENSMLUG00000017607	1 retrocopy	retro_mluc_2279,
Macaca mulatta	ENSMMUG00000021343	1 retrocopy	retro_mmul_2192,
Monodelphis domestica	ENSMODG00000000533	1 retrocopy	retro_mdom_414,
Ochotona princeps	ENSOPRG00000001701	1 retrocopy	retro_opri_1039 ,