RetrogeneDB ID: retro_opri_154

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_2970:49227..49716(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOPRG00000013234
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_154
TTGACGAAAGGAGAACTTCAGTGTCAGATTAGGGAGAGGCCCACACAGCTGGAGCAGATGTGTAGGGACATTGGCAACCG
ATTGTAGCCGACACATGTGTGACCCTGAAACAAAGAGACCATACATCGTTATTCTCATAGAGAGAGCCGTGAAAGGACAT
CCTCTATTCGGTCAAAACCAACAAGAGCACGAAACAGCGGCTTTGGAAGTGATCACGCAGCTGAGGGAGAAAATGAGGAT
AGAGCGCGCCCACGTGAGACTGCGGTTAATCCTCCTGGTGAATGAGGGCTACACGCTGAAGCAAAAGCTCAAGCAGCTCC
GCAAGGTCGTGGCAAGTGAGGACTGCTGTCAGCAGCTGGAAATGGTGTGCCTCATTGACCCCGCTGCTTCCTAGAAATCG
ATGAGCTCATAAAGAAGGAAGCCAAAGGCAGAGGTTCCTTGGAGGTGCTCAATCTCAAAGTCGTGGAAGAAGGCAACGAG
AAATTTGAA

Alignment

ORF - retro_opri_154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.33 %
• Parental protein coverage: 65.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LTKGELQVSDKERHTQLEQMFRD-IAT-IVADKCV-NPETKRPYTVILIERAMK-DIHYSVKTNKSTKQQ
          LTKGELQ....ER.TQLEQM.RD..AT.IVAD.CV..PETKRPY.VILIERA.K.DI.YSVKTNKSTKQ.
Retrocopy LTKGELQCQIRERPTQLEQMCRD>LAT>IVADTCV<DPETKRPYIVILIERAVK>DILYSVKTNKSTKQR

Parental  -ALEVIKQLKEKMKIERAHMRLRFILPVNEGKKLKEKLKPLIKVVESEDYSQQVEMVCLIDPG-CFREID
          .ALEVI.QL.EKM.IERAH.RLR.IL.VNEG..LK.KLK.L.KVV.SED..QQ.EMVCLIDP..CF.EID
Retrocopy <ALEVITQLREKMRIERAHVRLRLILLVNEGYTLKQKLKQLRKVVASEDCCQQLEMVCLIDPA<CFLEID

Parental  ELIKKETKGRGSLEVLSLKDVEEGDEKFE
          ELIKKE.KGRGSLEVL.LK.VEEG.EKFE
Retrocopy ELIKKEAKGRGSLEVLNLKVVEEGNEKFE

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_154 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,