RetrogeneDB ID: retro_opri_1086

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_68551:2..1283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAB1
• Ensembl ID: ENSOPRG00000015330
• Aliases: None
• Description: GRB2-associated binding protein 1 [Source:HGNC Symbol;Acc:4066]

Sequence

>retro_opri_1086
CTACACACCCAGGCATGGAAGAGAAGGTGGTTCGTGTTACGCAGTGGCCGTTTAACTGGAGATCCTGATGTGTTGGAATA
TTACAAAAATGATCATGCCAAGAAGCCAATTCGTATTATTGATTTAAATTTATGTCAGCAAGTTGATGCTGGATTGACAT
TTAATAAGAAAGAGTTTGAAAACCGCTACATTTTTTATATCAACACTATTGACCGGATTTTCTACTTGGTAGCAGACAGT
GAGGAGGAAATGAATAAGTGGGTTCGTTGCATTTGTGACATCTGTGGGTTTAATCCTACAGAAGAAGATCCTGTGAAGCT
GCCTGGTAGCTCCTTGCAAGCACAAGCTCATTTGCCCTTAGCTATAAACACAGCACCACCATCCTCCCAGATGGACTCCT
CCACTCTACCTCCTTCCTATCAGCTCATCAGCCTTCCGCCACCACATGCAGAAACTCTTGGCATCCAGGAGGATCCCCAA
GACTACCTCTTGCTAATCAACTGTCAAAGCAAGAAGCCTGAACCCACCAGAACACATGCCGACTCTGCAAAATCCACCTC
TTCTGAAACAGACTGTAATGATAACATCCCTTATCACAAAAATCCACCCTCCTCCCAGAGCAAACAGGGAGTGAATGGCT
TTTTCCAGCAGCAAATGCTGTATGACTCTCCCCCATCACGGGCTGCCTCTGTGTCCATAGACCCCAACCTTTACAACCTG
CCCAGGAGTTACTCTCATGATGTGCTACCAAAGGCATCTCCCTCAAGTACTGAAACAGATGGAGAACTCTATGTTTTTAA
TACCCCAACTGGGACATCAAGTATAGAGGCTCAAATGAGGCATGACTCCATCAGCTATGACATTCCTCCAACACCCGGTA
GTACTTACCAGGTTCCACGAACATTTCCTGATGGCACCTTGGGACAGACATCCAAGCTAGACACTATTCTTGATATCCCA
CCATCTCGGCCACCGAAGCCGCATCCAGCTCACGACAGATTTCCCGTGGAAATGTCTGGGCTCCCACGCACGACTTCCGA
CACCGACAGTAGCTACTGCATCCCTACAGCAGGGGTGCTGCCATCACGTAGTAATACCATTTCCACTGTGGAGCTGAACA
AATTGCGAAAAGATGCTAGTTCTCAAGACTGCTATGATGTTCCACGAACATTTCCAAGTGATAGATCTAGCTCACTTGAA
GGCTTCCATAATCACTTTAAAATCAAAAATGTGTTGACAGTGGGAAGTGTATCAAGTGAAGAACTGGATGAAAATTACGT
C

Alignment

ORF - retro_opri_1086 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.02 %
• Parental protein coverage: 59.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKRYAWKRRWFVLRSGRLTGDPDVLEYYKNDHAKKPIRIIDLNLCQQVDAGLTFNKKEFENRYIFYINTI
          L...AWKRRWFVLRSGRLTGDPDVLEYYKNDHAKKPIRIIDLNLCQQVDAGLTFNKKEFENRYIFYINTI
Retrocopy LHTQAWKRRWFVLRSGRLTGDPDVLEYYKNDHAKKPIRIIDLNLCQQVDAGLTFNKKEFENRYIFYINTI

Parental  DRIFYLVADSEEEMNKWVRCICDICGFNPTEEDPVKPPGSSLQAQADLPLAINTAPPSSQMDSSALPPSY
          DRIFYLVADSEEEMNKWVRCICDICGFNPTEEDPVK.PGSSLQAQA.LPLAINTAPPSSQMDSS.LPPSY
Retrocopy DRIFYLVADSEEEMNKWVRCICDICGFNPTEEDPVKLPGSSLQAQAHLPLAINTAPPSSQMDSSTLPPSY

Parental  QLISLPPPHAETLGIQEDPQDYLLLINCQSKKPEPTRTHADSAKSTSSETDCNDNVPSHKNPPSSQSKHG
          QLISLPPPHAETLGIQEDPQDYLLLINCQSKKPEPTRTHADSAKSTSSETDCNDN.P.HKNPPSSQSK.G
Retrocopy QLISLPPPHAETLGIQEDPQDYLLLINCQSKKPEPTRTHADSAKSTSSETDCNDNIPYHKNPPSSQSKQG

Parental  VNGFFQQQMLYDSPPSRAASVSIDPNLYNLPRSYSHDVLPKASPSSTETDGELYVFNTPSGTSSIEAQMR
          VNGFFQQQMLYDSPPSRAASVSIDPNLYNLPRSYSHDVLPKASPSSTETDGELYVFNTP.GTSSIEAQMR
Retrocopy VNGFFQQQMLYDSPPSRAASVSIDPNLYNLPRSYSHDVLPKASPSSTETDGELYVFNTPTGTSSIEAQMR

Parental  HVSISYDIPPTPGSTYQVPRTFPDGTLGQTSKLDTIPDIPPPRPPKPHPAHDRSPVETSGLPRTTSDTDS
          H.SISYDIPPTPGSTYQVPRTFPDGTLGQTSKLDTI.DIPP.RPPKPHPAHDR.PVE.SGLPRTTSDTDS
Retrocopy HDSISYDIPPTPGSTYQVPRTFPDGTLGQTSKLDTILDIPPSRPPKPHPAHDRFPVEMSGLPRTTSDTDS

Parental  SYCIPTAGVPPSRSNTISTVELNKLRKDASSQDCYDIPRTFPSDRSSSLEGFHNHFKIKNVLTVGSVSSE
          SYCIPTAGV.PSRSNTISTVELNKLRKDASSQDCYD.PRTFPSDRSSSLEGFHNHFKIKNVLTVGSVSSE
Retrocopy SYCIPTAGVLPSRSNTISTVELNKLRKDASSQDCYDVPRTFPSDRSSSLEGFHNHFKIKNVLTVGSVSSE

Parental  ELDENYV
          ELDENYV
Retrocopy ELDENYV

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_1086 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004704	2 retrocopies	retro_chof_1080, retro_chof_2144,
Ochotona princeps	ENSOPRG00000015330	1 retrocopy	retro_opri_1086 ,