RetrogeneDB ID: retro_opri_261

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4311:101889..102844(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TDP2
• Ensembl ID: ENSOPRG00000016299
• Aliases: None
• Description: tyrosyl-DNA phosphodiesterase 2 [Source:HGNC Symbol;Acc:17768]

Sequence

>retro_opri_261
GCGATGGCAAAGTGCTACCTGGCCGAGGACGACTGGGAGATGGAAAAGGCGCTGGACTCCTACTTCGAGCGGCCGGCAGA
GGAGAGCGCCTCGCAGAGCCGCCCGGTGGAGCCCGCGGCCTGCGTTGACCTCACCAATGAAGAAACAAGTGACTCCATTA
GTTCTAAAACCAGCTGTCCCAGACCACCGCGCAGGAAGATGGCAGCATGTTCTCTCTCATTACCTGGAACATTGATGGAT
TGGATCTAAACCACCTGCAAGAGAGGGCTCCGGGAGTGTGTTCCTAGCTAGCTTTGTACTGCCCAGATGTGATATTTCTA
CAGGAAGTAATCCCACCGTATTGCAGCTACCTAAAGAAGCGAGCAAGTAATTATGAAATTATTGCAGGTAATGAAGAAGG
ATATTTCACAGCTATAATGTTGAAGAAACCCAGAGTGAAATTAAAAAGCCAAGAGATAATTCCTTTTCCAAATACCAAAA
TGATGAGGAACCTTTTGTGTGTGCAGGTGAGTTTGTCCGGGAATGAGCTTTACCTTACGACCTCACATTTGGAGAGCACC
AGGGGCCATGCCATGGAATGAATTAATCAGTTCAAAGCGGTCCTACAGAAAAGCCAGGAGGCTCCCAAATCAGCTACTGT
TATATTTGCAGGAGAGACAAATTTAAGAGATCAAGAAGTTACCAAATGTGATGGTTTACCCAACAACATCTTGGATGTCT
GGGAGTTTCCGGGCAAACCTAAGCATTGCCAGCATACATGGGACACCCGAGTGAACTCTAATCTGGGTATAGCTGCTCCT
TGCAAGCTGCGTTTTGATTGGATATTCTTCAGAGCAGCAGCAGACGTGGGCCACATTATTCCCGAAGTTTGGACCTCCTT
GGGTTGGAAAAACTGGACTGTGGTAGATTTCCTAGTGATCACTGGGGCCTTCTGTGCAACTTGGATGTTATATTG

Alignment

ORF - retro_opri_261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.72 %
• Parental protein coverage: 91.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVAQCYLAENDWEMERALDSYFERPAEESASQSGPAEPAACVDLTSEETSDSISSKTS-QSETTVQEDGS
          A.A.CYLAE.DWEME.ALDSYFERPAEESASQS.P.EPAACVDLT.EETSDSISSKTS..S.TT.QEDGS
Retrocopy AMAKCYLAEDDWEMEKALDSYFERPAEESASQSRPVEPAACVDLTNEETSDSISSKTS<LSQTTAQEDGS

Parental  MFSLITWNIDGLDLNHLQERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRARDYEIIAGNEEGYFTAI
          MFSLITWNIDGLDLNHLQERA.GVCS.LALY.PDVIFLQEVIPPY.SYLKKRA..YEIIAGNEEGYFTAI
Retrocopy MFSLITWNIDGLDLNHLQERAPGVCS*LALYCPDVIFLQEVIPPYCSYLKKRASNYEIIAGNEEGYFTAI

Parental  MLKKSRVKLKSQEIIPFPNTKMMRNLLCVQVSLSGNELYLMTSHLESTRGHAVERMNQLKVVLQKIQEAP
          MLKK.RVKLKSQEIIPFPNTKMMRNLLCVQVSLSGNELYL.TSHLESTRGHA.E..NQ.K.VLQK.QEAP
Retrocopy MLKKPRVKLKSQEIIPFPNTKMMRNLLCVQVSLSGNELYLTTSHLESTRGHAME*INQFKAVLQKSQEAP

Parental  ESATVIFAGDTNLRDQEVTKCGGLPNNILDVWEFLGKPKHCQYTWDTRVNSNLGIAAPCKLRFDRIFFRA
          .SATVIFAG.TNLRDQEVTKC.GLPNNILDVWEF.GKPKHCQ.TWDTRVNSNLGIAAPCKLRFD.IFFRA
Retrocopy KSATVIFAGETNLRDQEVTKCDGLPNNILDVWEFPGKPKHCQHTWDTRVNSNLGIAAPCKLRFDWIFFRA

Parental  AADEGHIIP-RSLDLLGLEKLDCGRFPSDHWGLLCNLDVIL
          AAD.GHIIP.RSLDLLGLEKLDCGRFPSDHWGLLCNLDVIL
Retrocopy AADVGHIIP<RSLDLLGLEKLDCGRFPSDHWGLLCNLDVIL

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_261 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012012	2 retrocopies	retro_chof_2007, retro_chof_616,
Callithrix jacchus	ENSCJAG00000006074	1 retrocopy	retro_cjac_363,
Dasypus novemcinctus	ENSDNOG00000010113	1 retrocopy	retro_dnov_500,
Ochotona princeps	ENSOPRG00000016299	2 retrocopies	retro_opri_261 , retro_opri_939,