RetrogeneDB ID: retro_opri_1179

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_8885:25342..25835(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SBDS
• Ensembl ID: ENSOPRG00000008721
• Aliases: None
• Description: Shwachman-Bodian-Diamond syndrome [Source:HGNC Symbol;Acc:19440]

Sequence

>retro_opri_1179
ATGTCCATCTTCACCCCCACCAACCAGACCCACCTGACCAATGTGGCCGTGGCGTGGACAAAGTGCGTGGGCAAATGCTT
CGAGATCACCTGCTTTAAGAGCAGGGTGATTGGCTGGCGGACTGATGTGGACAAAGTCCTCGATGAAGTTCTGCAGACCC
ACTCGGTGTTTGTAAAAGTCTCTAAAGGTCAGGCTGCAAAGCAGGATGACCTCATCAACACGGTGGAACCAATGACCAAA
CTGAAATGTGCAAACAGATTTTGACTCAAGAAGAGCGTCAGGTGTCAGACAAGGAGAGGCACACACAGCTGGAGCAGATG
TTCAGGGTCGTTATAACTATTGCAGCTGAGAAACGTGTGAACCCTGAAGTGAGGACACACTACACCGTCGTTCTCATAGA
GCCGGGAAGGACATCCACTCTTCAGTCGAAACCAACAAGACCACGAAACAGCAGGCTTTGGAAGTAATCAAGTAGTTAAA
GGAGAAAATGAAG

Alignment

ORF - retro_opri_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.64 %
• Parental protein coverage: 66.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSIFTPTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRTGVEKDLDEVLQTHSVFVNVSKGQVAKKDD
          MSIFTPTNQ..LTNVAV...K..GK.FEI.C.K..V.GWRT.V.K.LDEVLQTHSVFV.VSKGQ.AK.DD
Retrocopy MSIFTPTNQTHLTNVAVAWTKCVGKCFEITCFKSRVIGWRTDVDKVLDEVLQTHSVFVKVSKGQAAKQDD

Parental  LISAF-GTDDQTEICRQILTKGELQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILI-ERAMK
          LI....GT.DQTE.C.QILT..E.QVSDKERHTQLEQMFR...TI.A.K.VNPE..R.........RA.K
Retrocopy LINTV<GTNDQTEMCKQILTQEERQVSDKERHTQLEQMFRVVITIAAEKRVNPEV-RTHYTVVL<HRAGK

Parental  DIHYSVKTNKSTKQQALEVIKQLKEKMK
          DIH.SV.TNK.TKQQALEVIK.LKEKMK
Retrocopy DIHSSVETNKTTKQQALEVIK*LKEKMK

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_1179 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003795	2 retrocopies	retro_chof_1999, retro_chof_623,
Callithrix jacchus	ENSCJAG00000004283	1 retrocopy	retro_cjac_3984,
Dasypus novemcinctus	ENSDNOG00000016904	1 retrocopy	retro_dnov_748,
Loxodonta africana	ENSLAFG00000008763	1 retrocopy	retro_lafr_920,
Monodelphis domestica	ENSMODG00000006644	1 retrocopy	retro_mdom_2004,
Mus musculus	ENSMUSG00000025337	1 retrocopy	retro_mmus_950,
Otolemur garnettii	ENSOGAG00000009011	1 retrocopy	retro_ogar_3368,
Ochotona princeps	ENSOPRG00000008721	6 retrocopies	retro_opri_1179 , retro_opri_154, retro_opri_363, retro_opri_484, retro_opri_698, retro_opri_957,
Rattus norvegicus	ENSRNOG00000000888	1 retrocopy	retro_rnor_686,
Ictidomys tridecemlineatus	ENSSTOG00000022203	1 retrocopy	retro_itri_1763,