RetrogeneDB ID: retro_opri_242

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4158:84846..85900(+)
• Located in intron of: ENSOPRG00000004660

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK1
• Ensembl ID: ENSOPRG00000014484
• Aliases: None
• Description: mitogen-activated protein kinase 1 [Source:HGNC Symbol;Acc:6871]

Sequence

>retro_opri_242
CCGAAAATTGTCAGCGGGCAGGGTTCCGACGTGGGGGCCTACCTACCCAAACCTCTTCTTCCTCGGCGGAGGGGGCCTAC
GGCATGGTGTGCTTTTGCTTATGATAACGTCAACAAAGTTCGAGTGGCTATCAAAGAAAATCAGTCCTTTTGAGCACCAG
ACCTATTGCCAGAGGACCCTGAGGGAGATCAAGATCTTGCTGCGTTTCAGACATGAACACATCATTGGGATCAATGACAT
CATCCGCGCACCGACCATCGAGCAGATGAAAGATGTATACATAGTACAGGACCTAATGGAGACAGATCTCTACAAGTTCT
TGAAGACACAGCACCTCAGCAACGACCATATCTGCTATTTTCTTTACCAGATCCTGCGAGGATTAAAATACATTCACTCA
GCTAACGTTCTGCACCGCGACCTCAAGCCTTCCAACCTGCTGCTCAACACCACCTGTGATCTCAAGATCTGTGACTTTGG
CTTGGCCCGCTTTGCAGATCCGGACAACGACCACACAGGGTTCCTGACAGAGTATGTAGCCACCCGTTGGTACAGGGCTC
CAGAAATTATGTTGAATTCCAAGGGCTACACCAAGTCCATCGACATCTGGTCTGTGGGCTGCATGCTGGCGGAGATGCTC
TCCAACCGGCCCATCTTCCCGGGGAAGCACTACCTCGACCAGCTGAACCACATTCTGGGTATTCTTGGTTCCCCATCACA
AGAAGACCTGAACTGTATAATAAATTTAAAAGCTAGAAACTATTTGCTTTCTCTTCCACACAAAAACAAGGTGCCATGGA
ACAGGTTGTTCCCAAATGCCAACTCCAAAGCTCTGGACTTGCTGGACAAAATGTTGACATTCAACCCTCACAAGAGGATC
GAGGTCGAACAGGCTCTGGCGCACCCCTATCTGGAGCAATATTATGACCCCAGTGACGAGCCAATTGCCGAAGCTCCATT
CAAGTTTGACTTGGAATTAGATGACTTGCCCAAGGAAAAACTCAAGGAGCTCATTTTTGAAGAGACTGCAAGATTCCAGC
CAGGATACAGATCT

Alignment

ORF - retro_opri_242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.79 %
• Parental protein coverage: 97.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PEMVRGQVFDVG-PRYTNLSYIG-EGAYGMVCS-AYDNVNKVRVAIK-KISPFEHQTYCQRTLREIKILL
          P..V.GQ..DVG.P.Y.NL...G.EGAYGMVC..AYDNVNKVRVAIK.KISPFEHQTYCQRTLREIKILL
Retrocopy PKIVSGQGSDVG>PTYPNLFFLG>EGAYGMVCF>AYDNVNKVRVAIK>KISPFEHQTYCQRTLREIKILL

Parental  RFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVL
          RFRHE.IIGINDIIRAPTIEQMKDVYIVQDLMETDLYK.LKTQHLSNDHICYFLYQILRGLKYIHSANVL
Retrocopy RFRHEHIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKFLKTQHLSNDHICYFLYQILRGLKYIHSANVL

Parental  HRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGC
          HRDLKPSNLLLNTTCDLKICDFGLAR.ADPD.DHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGC
Retrocopy HRDLKPSNLLLNTTCDLKICDFGLARFADPDNDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGC

Parental  ILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKA
          .LAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNA.SKA
Retrocopy MLAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNANSKA

Parental  LDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQP
          LDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFD.ELDDLPKEKLKELIFEETARFQP
Retrocopy LDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDLELDDLPKEKLKELIFEETARFQP

Parental  GYRS
          GYRS
Retrocopy GYRS

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_242 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010312	1 retrocopy	retro_btau_498,
Ficedula albicollis	ENSFALG00000007935	1 retrocopy	retro_falb_19,
Gallus gallus	ENSGALG00000001501	1 retrocopy	retro_ggal_20,
Myotis lucifugus	ENSMLUG00000005952	1 retrocopy	retro_mluc_302,
Monodelphis domestica	ENSMODG00000017722	1 retrocopy	retro_mdom_101,
Ochotona princeps	ENSOPRG00000014484	2 retrocopies	retro_opri_242 , retro_opri_615,