RetrogeneDB ID: retro_opri_885

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_4099:87553..87981(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIPRL
• Ensembl ID: ENSOPRG00000011313
• Aliases: None
• Description: TIP41, TOR signaling pathway regulator-like (S. cerevisiae) [Source:HGNC Symbol;Acc:30231]

Sequence

>retro_opri_885
ATACCACCCTTTAAAGGTGATCTTTATATGGAGAAGTTGAAAGCCAGAGAGCAGATTAAATTTTTCGAGGAAGTGCTTCT
GTTTGAGGACGGACTTCATGATCATGGGATTTCAAGCTTGAGTGTGAAAATTAGAGTGATGCCTACTAGCTTTTTCCTGC
TGTTGCGACTTTTTCTGCGAATCGATGGGGTGCCTATCAGAGGAATGACACAAGGCTTTACCATGAGGCTGACTAGACCT
ACATGCTACAAGAATATGCATCACGAGAAAGCAAAATTGCTAATTTAATGCATGTTTCACCTTCTCTCTTCACGGAACCT
AATGAAATATCACAGTATTTACCAATAAAGGAAGCAGTTTGTGAGAAGCTAATATTTCCAGAAGGAACCGACACTAACCC
TACTGACTCCCAAGAAAGTGCACCTCTA

Alignment

ORF - retro_opri_885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 52.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVPTTDHIDTEKLKAREQIKFFEEVLLFEDELHDHGVSSLSVKIRVMPTSFFLLLRFFLRIDGVLIR-MN
          ..P.......EKLKAREQIKFFEEVLLFED.LHDHG.SSLSVKIRVMPTSFFLLLR.FLRIDGV.IR..N
Retrocopy IPPFKGDLYMEKLKAREQIKFFEEVLLFEDGLHDHGISSLSVKIRVMPTSFFLLLRLFLRIDGVPIR<RN

Parental  DTRLYHEADKTYMLREYTSRESKIANLMHVSPSLFTEPNEISQYLPIKEAVCEKLIFPERIDPNPADSQE
          DTRLYHEAD.TYML.EY.SRESKIANLMHVSPSLFTEPNEISQYLPIKEAVCEKLIFPE..D.NP.DSQE
Retrocopy DTRLYHEAD*TYMLQEYASRESKIANLMHVSPSLFTEPNEISQYLPIKEAVCEKLIFPEGTDTNPTDSQE

Parental  GAPV
          .AP.
Retrocopy SAPL

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_885 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008689	3 retrocopies	retro_chof_1079, retro_chof_1094, retro_chof_1746,
Cavia porcellus	ENSCPOG00000009945	1 retrocopy	retro_cpor_763,
Echinops telfairi	ENSETEG00000005808	1 retrocopy	retro_etel_1273,
Microcebus murinus	ENSMICG00000007808	1 retrocopy	retro_mmur_1335,
Myotis lucifugus	ENSMLUG00000011927	3 retrocopies	retro_mluc_607, retro_mluc_909, retro_mluc_941,
Monodelphis domestica	ENSMODG00000002880	1 retrocopy	retro_mdom_180,
Mus musculus	ENSMUSG00000040843	1 retrocopy	retro_mmus_2653,
Ochotona princeps	ENSOPRG00000011313	1 retrocopy	retro_opri_885 ,
Pteropus vampyrus	ENSPVAG00000005071	1 retrocopy	retro_pvam_257,
Rattus norvegicus	ENSRNOG00000003048	1 retrocopy	retro_rnor_2197,
Sarcophilus harrisii	ENSSHAG00000018932	1 retrocopy	retro_shar_771,
Ictidomys tridecemlineatus	ENSSTOG00000014921	1 retrocopy	retro_itri_1756,
Tupaia belangeri	ENSTBEG00000017081	3 retrocopies	retro_tbel_1717, retro_tbel_2833, retro_tbel_3376,