RetrogeneDB ID: retro_opri_640

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_21150:781..1073(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR4
• Ensembl ID: ENSOPRG00000003476
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 4 [Source:HGNC Symbol;Acc:33772]

Sequence

>retro_opri_640
ATGACTTCTGCACTGATGCAGGGTCTGGAGGGAATCCCAGACCAGCTGGGCTAACTATGTTGAGGGAGGGTACAGTGTTG
TCTTTCTCCAGGGACCTCAGGAAGATAAGCAGGTGGCCAGTGTTATCACCAAACTGGTCGGCACAGCCTGTGGTTTTGAG
CTGCACCATGGCATGAACTTCTGCAAGTAGCTATCTGTGTTCTTTGGAGGGCATACGTTGCTGGTAACCATGTGGGGACA
GAGTATGTTTGTGGTGAAGTGGCAGAACTGAAGCCAGGATCCCACTGACATC

Alignment

ORF - retro_opri_640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTSALTQGLERIPDQLGYL-VLSEGAVLASSGDL-ENDEQAASAISELVSTACGFRLHHGMNVPFKRLSV
          MTSAL.QGLE.IPDQLG.L..L.EG.VL..S.DL...D.Q.AS.I..LV.TACGF.LHHGMN...K.LSV
Retrocopy MTSALMQGLEGIPDQLG*L<MLREGTVLSFSRDL<QEDKQVASVITKLVGTACGFELHHGMNF-CK*LSV

Parental  VFGEHTLLVTVSGQRVFVVKRQNRGREPIDV
          .FG.HTLLVT..GQ..FVVK.QN....P.D.
Retrocopy FFGGHTLLVTMWGQSMFVVKWQN*SQDPTDI

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_640 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014561	1 retrocopy	retro_cfam_1491,
Cavia porcellus	ENSCPOG00000013370	1 retrocopy	retro_cpor_119,
Mus musculus	ENSMUSG00000050552	1 retrocopy	retro_mmus_3544,
Ochotona princeps	ENSOPRG00000003476	1 retrocopy	retro_opri_640 ,
Pteropus vampyrus	ENSPVAG00000011987	1 retrocopy	retro_pvam_1449,