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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGTCGCATGGCCTCTTTGACGTGCGGGTAAAGGCCAAAGGAGACACTCACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttctttcctctttctcctcccttgttcattgatgaagagggaatatgctgaggtcttcgtcgaaattggtaaacatggctggcagtgagacat...

Basic information

species Physcomitrella patens
transcript PP1S37_83V6.1
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|162196840|gb|FC373895.1|FC373895
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162222109|gb|FC397337.1|FC397337
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162153154|gb|FC329560.1|FC329560
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162196839|gb|FC373894.1|FC373894
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162189059|gb|FC365177.1|FC365177
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTTCTAAA-GCTCTAGGTGACCGCAAGGGCA
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTT-CTAAAAGCTCTAGGTGACCGCAAGGGCA
EST: gi|18337884|gb|BJ169908.1|BJ169908
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162222108|gb|FC397336.1|FC397336
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162153155|gb|FC329561.1|FC329561
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCA-GGGCATA
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATA
EST: gi|208361844|gb|DC950116.1|DC950116
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162208762|gb|FC384898.1|FC384898
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162208763|gb|FC384899.1|FC384899
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCG
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCG
EST: gi|162271019|gb|FC447424.1|FC447424
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|37838754|gb|BJ596762.1|BJ596762
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162271020|gb|FC447425.1|FC447425
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAAGCGCTTCCGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162150420|gb|FC326692.1|FC326692
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGAT
EST: gi|162150421|gb|FC326693.1|FC326693
EST:     ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACT                         GCGCTTCTAAAAGCTCTAG
genomic: ACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAG

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), 17 (downstream exon)
Score: 5

GGCGTCGCATGGCCTCTTTGACGTGCGGGTAAAGGCCAAAGGAGACACTCACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttc ... gtgaattcagGCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGTCGCATGGCCTCTTTGACGTGCGGGTAAAGGCCAAAGGAGACACTCACATTGACGATCATCATACGAATGAGGATGTCGGCCTTGCTATGGGCACTgtatgtgttctttcctctttctcctcccttgttcattgatgaagagggaatatgctgaggtcttcgtcgaaattggtaaacatggctggcagtgagacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG