RetrogeneDB ID: retro_opri_846

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_36518:257..1349(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP2K1
• Ensembl ID: ENSOPRG00000007770
• Aliases: None
• Description: mitogen-activated protein kinase kinase 1 [Source:HGNC Symbol;Acc:6840]

Sequence

>retro_opri_846
AACCTGGTGGACCTGCACAAGAAGCTTGAGGAGCTTGAGTTAGACGAGCAGCAGAGGCGGCGCCTGGAGGCCTTCCTCAC
CCAGAAGGCCAAGGTCGGCGAGCTCAAGGAGGATGACTTTGAAAGGTTCTCAGAGCTGGGGGCCGGCAGTGGCGGCGTGG
TCACCAAGGTGCGGCACCGGCCTCGGGGCTTATCATGGCCAGGAAGCTGATCCACCTAGAGATCAAGCCGGCCACCCGGA
ACCAGATCAGCCGTGAGCTGCAGGTGCTGCATGAGTGCAACTCGTCCTACATCGTGGGCTTCTACGGGGCCTTCTACAGC
AACGGCGAGATCAGTATATGCATGGAGCACATGGACGGCGGCTCCCTGGACCAGGTGCTGAAGGAGGCCCAGAGGATTCC
GGAAGAGATCCTGGGCAAAGTCAGCATTGCAGTCCTCCGGGGTCTGGCGTATCTCCGAGAGAAAGACCAAATCATGCATC
GAGAAGTAAAGCCCTCCAACATTCTGGTCAACTTCCGGGACCAGATCAAGCTGTTCGACTTCGGCGTCAGCGGGCAGCTC
ATCGACTCCATGACCAACTCCTTCGTGGGCACCCGCTCCTACATGTCTCCGGAGCGGCTGCAGGGCACCCACTACTCGGT
ACAGTCGGATATCTGGAGCATGGGCCTGTCCCTGGTGGAGCTGGCCATCGGCAGGTATCCCGTCCCCCCACTGGACGCCA
AGGAGCTCGAGGCCACGTTCGGCTGGCCCATGGTGGACGCGGCGGACACAGAGCCTCACAGCACCTCACCTCGCCCACGG
CCCCCAGGACGCCCCGTCAGCGGTCACGGGGTGGACAGCCGGCCAGCCATGGCCATCTTCGAACTACTGGACTACATGGT
GAATGAGCCACCTCCCAAACTGCCCAGCAGCGTGTTCACCGCCGACTTCCAGGAGTTTGTAAATAAATGCCTCATCAAGA
ACCCGGCAGAACAAGCAGACCTCAAGATGCTCATGAACCACACCTTCATCAAGCGTCCGAGGTAGAGGAAGTGGACTTTG
CTGGCTGGCTTTGTGAGACCCTGCGCTGAAGCAGCCCAGTACGCCCACGCAC

Alignment

ORF - retro_opri_846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 98.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NLEALQKKLEELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKP-SGLVMARK
          NL..L.KKLEELELDEQQR.RLEAFLTQK.KVGELK.DDFE..SELGAG.GGVV.KV.H.P.SGL.MARK
Retrocopy NLVDLHKKLEELELDEQQRRRLEAFLTQKAKVGELKEDDFERFSELGAGSGGVVTKVRHRP<SGLIMARK

Parental  LIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILG
          LIHLEIKPA.RNQI.RELQVLHECNS.YIVGFYGAFYS.GEISICMEHMDGGSLDQVLK.A.RIPE.ILG
Retrocopy LIHLEIKPATRNQISRELQVLHECNSSYIVGFYGAFYSNGEISICMEHMDGGSLDQVLKEAQRIPEEILG

Parental  KVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQG
          KVSIAV..GL.YLREK..IMHR.VKPSNILVN.R..IKL.DFGVSGQLIDSM.NSFVGTRSYMSPERLQG
Retrocopy KVSIAVLRGLAYLREKDQIMHREVKPSNILVNFRDQIKLFDFGVSGQLIDSMTNSFVGTRSYMSPERLQG

Parental  THYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELLFGCQVEGEAAETP----ARPRTPGRPLSSYGMD
          THYSVQSDIWSMGLSLVE.A.GRYP.PP.DAKELE..FG......A...P.....RPR.PGRP.S..G.D
Retrocopy THYSVQSDIWSMGLSLVELAIGRYPVPPLDAKELEATFGWPMVDAADTEPHSTSPRPRPPGRPVSGHGVD

Parental  SRPPMAIFELLDYIVNEPPPKLPSAVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKR-SDAEEVDFA
          SRP.MAIFELLDY.VNEPPPKLPS.VF...FQ.FVNKCLIKNPAE.ADLK.LM.H.FIKR.S..EEVDFA
Retrocopy SRPAMAIFELLDYMVNEPPPKLPSSVFTADFQEFVNKCLIKNPAEQADLKMLMNHTFIKR<SEVEEVDFA

Parental  GWLCSTI-GLNQPSTPTH
          GWLC.T...L.QPSTPTH
Retrocopy GWLCETL<ALKQPSTPTH

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_846 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033983	1 retrocopy	retro_btau_1416,
Cavia porcellus	ENSCPOG00000003053	1 retrocopy	retro_cpor_483,
Gorilla gorilla	ENSGGOG00000003687	1 retrocopy	retro_ggor_2650,
Macaca mulatta	ENSMMUG00000016840	1 retrocopy	retro_mmul_2285,
Otolemur garnettii	ENSOGAG00000015876	1 retrocopy	retro_ogar_1598,
Ochotona princeps	ENSOPRG00000007770	1 retrocopy	retro_opri_846 ,
Pongo abelii	ENSPPYG00000006576	2 retrocopies	retro_pabe_3092, retro_pabe_3249,
Pan troglodytes	ENSPTRG00000007193	1 retrocopy	retro_ptro_2676,