RetrogeneDB ID: retro_opri_105

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2334:185804..186201(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAK1
• Ensembl ID: ENSOPRG00000001127
• Aliases: None
• Description: BCL2-antagonist/killer 1 [Source:HGNC Symbol;Acc:949]

Sequence

>retro_opri_105
ATGGCATCCGGGCCAGGCCCAGGCCCACCCAGCGAGGGTGCGATGAGGCTTCCAAACCCCCGAATTACAAGCAGCAGGTA
GCATAGGACTCAGAGGAAGTTTTGCACAGCTACGTGTTTTACCGGCACCAGCAGGAGCAGGAGACCAAGGGGGCAGCCAC
CCCCGTTGACCCCGAAATGGCCTCCGGGCACCCAGCACCTAACAGCATCCTGGGGCAGGTGGGGTGATAGCTTGCCATCA
TCGAGGACAACATCAACCAGCGCTATGACTTGGACTTCCAGAGCATCTGGAAAAGCAGCAGTCCACAGCGGAGAACGCCT
ATGAGATGTTCAAGATAGCTTCAAGCCTGTTTGAGAGCGGCATCAGCTGGGGAAGGGCGGTGGCCTTCCTGAGTTTC

Alignment

ORF - retro_opri_105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 63.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASGQSPGPPSEG-CDEPSQPRNSEQQVVQDSEEVFRSYVFYRHQQEQETEGAAAPVDPEMASWHPAPNS
          MASG..PGPPSEG.CDE.S.P.N..QQV..DSEEV..SYVFYRHQQEQET.GAA.PVDPEMAS.HPAPNS
Retrocopy MASGPGPGPPSEG<CDEASKPPNYKQQVA*DSEEVLHSYVFYRHQQEQETKGAATPVDPEMASGHPAPNS

Parental  MMAQVGRQLAFIGDDINQRYEADFQSI-LEKLQPTAENAYELFIKIASSLFESGINWGRVVALLGF
          ...QVG..LA.I.D.INQRY..DFQSI.LEK.Q.TAENAYE.F.KIASSLFESGI.WGR.VA.L.F
Retrocopy ILGQVG**LAIIEDNINQRYDLDFQSI<LEKQQSTAENAYEMF-KIASSLFESGISWGRAVAFLSF

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_105 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013657	1 retrocopy	retro_fcat_202,
Homo sapiens	ENSG00000030110	2 retrocopies	retro_hsap_2468, retro_hsap_942,
Gorilla gorilla	ENSGGOG00000022462	1 retrocopy	retro_ggor_761,
Macaca mulatta	ENSMMUG00000009104	1 retrocopy	retro_mmul_1130,
Nomascus leucogenys	ENSNLEG00000008351	1 retrocopy	retro_nleu_296,
Ochotona princeps	ENSOPRG00000001127	2 retrocopies	retro_opri_105 , retro_opri_938,
Pan troglodytes	ENSPTRG00000018053	1 retrocopy	retro_ptro_652,