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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGAGCTCCTCATTATGATCGATGCATGCCGCCGAGCTTCTGCTAAGAACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttcatattacatcactatgttctcttgatctgcatttcattctttgacttgaacaccatccgcaagagtcgtcaatagatattctcttgacata...

Basic information

species Physcomitrella patens
transcript PP1S42_193V6.4
intron # 3
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|100383515|gb|BY950299.1|BY950299
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|100356373|gb|BY946332.1|BY946332
EST:     ACGTAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|100360321|gb|BY966113.1|BY966113
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAGATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|100352263|gb|BY983120.1|BY983120
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTANA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCNAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|100399937|gb|BY990696.1|BY990696
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|162261958|gb|FC436817.1|FC436817
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|100354646|gb|BY983494.1|BY983494
EST:     CATAACAGCTGTGATACCATACTTTGGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGAGGAGAATCTATTGCTGCCAAGCTAGGTTGCAAATTTTATCAC
genomic: CATAACAGCTGTGATACCATACTTTGG-TTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAG-TTGCAAATTTAATCAC
EST: gi|100353033|gb|BY945573.1|BY945573
EST:     CATAACAGCTGTGATACCATACTTTTGGT-ATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTANGT-GCAAATTTAATCAC
genomic: CATAACAGCTGTGATACCATACTTT-GGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTA-GTTGCAAATTTAATCAC
EST: gi|100389903|gb|BY971255.1|BY971255
EST:     ACATAACAGCTGTGATACCATACTTTGGGTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCAC
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCAC
EST: gi|208380333|gb|DC907658.1|DC907658
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|208357746|gb|DC902298.1|DC902298
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|100372888|gb|BY948750.1|BY948750
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|19780598|gb|BQ039579.1|BQ039579
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|100441557|gb|BY980979.1|BY980979
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCANGGACGANGA-TCTATTGCTGCCAAGCTAGTTGCAAATTTTATCAC
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGA-GAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCAC
EST: gi|208399184|gb|DC912427.1|DC912427
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|67573736|gb|BJ946560.1|BJ946560
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|100429179|gb|BY977979.1|BY977979
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCNAGCTANGT-GCAAATTTNATCAC
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTA-GTTGCAAATTTAATCAC
EST: gi|100353317|gb|BY964745.1|BY964745
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
EST: gi|162258694|gb|FC434389.1|FC434389
EST:     ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAA                         ACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT
genomic: ACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 31 (upstream exon), 26 (downstream exon)
Score: 4

GATGGAGCTCCTCATTATGATCGATGCATGCCGCCGAGCTTCTGCTAAGAACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttca ... tggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGAGCTCCTCATTATGATCGATGCATGCCGCCGAGCTTCTGCTAAGAACATAACAGCTGTGATACCATACTTTGGTTATGCTCGAGCAGATCGTAAAgtgagtttcatattacatcactatgttctcttgatctgcatttcattctttgacttgaacaccatccgcaagagtcgtcaatagatattctcttgacata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT