RetrogeneDB ID: retro_opri_342

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_545:878065..878575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL12B
• Ensembl ID: ENSOPRG00000009826
• Aliases: None
• Description: myosin, light chain 12B, regulatory [Source:HGNC Symbol;Acc:29827]

Sequence

>retro_opri_342
AGCAAAAAGGCCAAGATGAAGCCCACCGAGAAGGGCCCTTGGTGCGCAACATCCAAGGTGTCCGCCACGTGTGTCCAGGC
ACACATCCAGGAGTTCAAAGAGGTCTTCAGCATGACTGATCAGAATCGAGACAGCTACACTGACAAGGAGGATCTGCGTG
ACAGGCTTGCCTCACTGGGGAGGAATCTCACTGATGCATACCTGAGTGCCGTGAAGAACCAGGCACCAGGCCCCATCACT
CTCACCATGTTCCTCACCATGTCTGGAGAAAAGCTGGACAGCACAGACCCTGAGGTTGTCATCCAAAATGCCTTTGCATG
CTCTGATGAGGAAGCCACGGGCTTCATTCAGGAGGACCATCTGCAAGAGCTGCTGACAACCATGGGGGACCACTTTAAAG
ACAAGCTAGTGGACAAGCTCTACAGAGAAGCTCCTGTTAACAAAAAGAGGACTTGCAATTACATCAAGTTCACTTGTATC
CTTAAACACTGAGCAAAGGACAAGGATGAC

Alignment

ORF - retro_opri_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.41 %
• Parental protein coverage: 98.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKKAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDEYLDA
          SKKAK.K.T.K.P..ATS.V.A...Q..IQEFKE.F.M.DQNRD...DKEDL.D.LASLG.N.TD.YL.A
Retrocopy SKKAKMKPTEKGPWCATSKVSATCVQAHIQEFKEVFSMTDQNRDSYTDKEDLRDRLASLGRNLTDAYLSA

Parental  MMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTTMGDRFTDEEVDEL
          ..N.APGPI..TMFLTM.GEKL..TDPE.VI.NAFAC.DEEATG.IQED.L.ELLTTMGD.F.D..VD.L
Retrocopy VKNQAPGPITLTMFLTMSGEKLDSTDPEVVIQNAFACSDEEATGFIQEDHLQELLTTMGDHFKDKLVDKL

Parental  YREAPIDKKGNFNYIEFTRILKHGAKDKDD
          YREAP..KK...NYI.FT.ILKH.AKDKDD
Retrocopy YREAPVNKKRTCNYIKFTCILKH*AKDKDD

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_342 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000006985	1 retrocopy	retro_eeur_311,
Gorilla gorilla	ENSGGOG00000004051	4 retrocopies	retro_ggor_1139, retro_ggor_1140, retro_ggor_2330, retro_ggor_2675,
Ochotona princeps	ENSOPRG00000009826	2 retrocopies	retro_opri_342 , retro_opri_736,