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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataattagccaggtctatttgttggtattgaaaggtttatagtactcaaggtagtaccatgattttatcacaatcctgaaaagttggttttcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG

Basic information

species Physcomitrella patens
transcript PP1S79_254V6.2
intron # 3
splice site 3'
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|100398771|gb|BY990507.1|BY990507
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100398308|gb|BY972539.1|BY972539
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|208395729|gb|DC911822.1|DC911822
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18375106|gb|BJ206684.1|BJ206684
EST:     CCTTCTTGGAGTATGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: CCTTCTTGGAGTA-GTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18372904|gb|BJ204506.1|BJ204506
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18358733|gb|BJ190792.1|BJ190792
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100404436|gb|BY973577.1|BY973577
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100422683|gb|BY957948.1|BY957948
EST:     TCCTTCTTGGAGTAGTCGCAAAAGCTGTTGATGAAGAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACCCCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|208346919|gb|DC905449.1|DC905449
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|208400165|gb|DC904813.1|DC904813
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18352604|gb|BJ184658.1|BJ184658
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18343422|gb|BJ175460.1|BJ175460
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|208350210|gb|DC901594.1|DC901594
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100407245|gb|BY974075.1|BY974075
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18364014|gb|BJ196087.1|BJ196087
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18368897|gb|BJ200982.1|BJ200982
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100363297|gb|BY984455.1|BY984455
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100390136|gb|BY989216.1|BY989216
EST:     CCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGT-GCCCTC-AAG                         ATTGATTCTGTGGTGACACCTAA
genomic: CCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCC-TCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAA
EST: gi|18357173|gb|BJ189232.1|BJ189232
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGT
EST: gi|100437331|gb|BY961467.1|BY961467
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|208398960|gb|DC912119.1|DC912119
EST:     TCCTTCTTGGAGTANTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100439349|gb|BY980219.1|BY980219
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|208391691|gb|DC942281.1|DC942281
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100353619|gb|BY964897.1|BY964897
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18354389|gb|BJ186445.1|BJ186445
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100399784|gb|BY972891.1|BY972891
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCCAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18345187|gb|BJ177228.1|BJ177228
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|208378690|gb|DC914664.1|DC914664
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18356417|gb|BJ188476.1|BJ188476
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100432416|gb|BY960464.1|BY960464
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100408155|gb|BY955925.1|BY955925
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|100413319|gb|BY956613.1|BY956613
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
EST: gi|18361754|gb|BJ193821.1|BJ193821
EST:     TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG                         ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT
genomic: TCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTT

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: 34 (upstream exon), 18 (downstream exon)
Score: 4

GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAGgtatctcttt ... tcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaggtagtaccatgattttatcacaatcctgaaaagttggttttcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG
                                          ttttctt  CT-rich tract
 atgattttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataattagccaggtctatttgttggtattgaaaggtttatagtactcaaggtagtaccatgattttatcacaatcctgaaaagttggttttcttgggcagATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG