RetrogeneDB ID: retro_opri_354

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_720:208519..209213(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT8
• Ensembl ID: ENSOPRG00000013065
• Aliases: None
• Description: CCR4-NOT transcription complex, subunit 8 [Source:HGNC Symbol;Acc:9207]

Sequence

>retro_opri_354
GACACCGAGTTTCCAGGTGTGGTTGCAAGACCTATTGGTGAATTCAGGAGCAATGCTGGCTATCAGTACCAACTGTTGCG
GTGTAACGTAGACTTGCTAAAGATAATTCAGCTAGGACTGACCTTTATGGATGAGCAGGAGATACCCGCCAGGAACTTCA
CTTGGCAGTTTAATTTTAAATTTAATTTGACGGAGGACATGTATGCCCAGGACTCAATAGAGCTGCTAACAACATCTGGT
ATCCAATTTAAAAAACATGAAGAGGCAGGAATTGAGACCCAGTACTTTGCAGAACTTCTAATGACTTCCGGAGTGGTCCT
TTGTGAAGGGGTCAAATGGTTATCATTTCATAGCGGTTATGACTTTGGCTATTTAATAAAAATCCTGACAAACTCTAATT
TGCCTGAAGAAGAACGTTGATTTCTTTGAGATCCTTCGGTTGTTTTTTCCTGTCATTTATGACGTGAAATACCTCATGGA
GAGCTGCAAAAATCTCAAGGGTGGATTGCAAGAAGATGCTGAACAGTTAGAGCTGGAACGGATAGGACCACAGCATCAGG
CAGGATCTGATTCATTGCTCACAGGAATGGCCTTTTTCAAAATGAGAGAAATGTTCTTTGAAGATCATATTGATAATGCC
AAATATTGTGGTCATTTGTATGGCCTTGGTTCTGGTTCATCCCATGTACAGAAC

Alignment

ORF - retro_opri_354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.25 %
• Parental protein coverage: 91.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DTEFPGVVVRPIGEFRSSIDYQYQLLRCNVDLLKIIQLGLTFTNEKGEYPSGINTWQFNFKFNLTEDMYS
          DTEFPGVV.RPIGEFRS...YQYQLLRCNVDLLKIIQLGLTF..E..E.P....TWQFNFKFNLTEDMY.
Retrocopy DTEFPGVVARPIGEFRSNAGYQYQLLRCNVDLLKIIQLGLTFMDEQ-EIPARNFTWQFNFKFNLTEDMYA

Parental  QDSIDLLANSGLQFQKHEEEGIDTLHFAELLMTSGVVLCDNVKWLSFHSGYDFGYMVKLLTDSRLPEEEH
          QDSI.LL..SG.QF.KHEE.GI.T..FAELLMTSGVVLC..VKWLSFHSGYDFGY..K.LT.S.LPEEE.
Retrocopy QDSIELLTTSGIQFKKHEEAGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEER

Parental  -EFFHILNLFFPSIYDVKYLMKSCKNLKGGLQEVADQLDLQRIGRQHQAGSDSLLTGMAFFRMKELFFED
          ..FF.IL.LFFP.IYDVKYLM.SCKNLKGGLQE.A.QL.L.RIG.QHQAGSDSLLTGMAFF.M.E.FFED
Retrocopy >DFFEILRLFFPVIYDVKYLMESCKNLKGGLQEDAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFED

Parental  SIDDAKYCGRLYGLGTGVAQKQN
          .ID.AKYCG.LYGLG.G....QN
Retrocopy HIDNAKYCGHLYGLGSGSSHVQN

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_354 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014232	1 retrocopy	retro_dnov_446,
Macropus eugenii	ENSMEUG00000007427	8 retrocopies	retro_meug_1667, retro_meug_1677, retro_meug_1931, retro_meug_2053, retro_meug_350, retro_meug_420, retro_meug_487, retro_meug_88,
Ochotona princeps	ENSOPRG00000013065	4 retrocopies	retro_opri_215, retro_opri_354 , retro_opri_632, retro_opri_795,