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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggcagttgggaatcaaggttgcttcgcctttacacacacacacacttagcccgacagttctcttatcggtcgtcgatttcctttggtgtttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCTGGGAGATGAGTTTAAGGGGTATGTCTTCAAGATTATGGGAGGTTGCGAC

Basic information

species Physcomitrella patens
transcript PP1S253_7V6.1
intron # 2
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|208389914|gb|DC937745.1|DC937745
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|18358411|gb|BJ190470.1|BJ190470
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACAACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|67572029|gb|BJ944853.1|BJ944853
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|162208309|gb|FC384621.1|FC384621
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|18353279|gb|BJ185334.1|BJ185334
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGC
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGC
EST: gi|18374956|gb|BJ206534.1|BJ206534
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|67577618|gb|BJ949785.1|BJ949785
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|18371412|gb|BJ203014.1|BJ203014
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|67702716|gb|BJ962949.1|BJ962949
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCNAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|100412712|gb|BY974870.1|BY974870
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|67702230|gb|BJ962463.1|BJ962463
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCNAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|67704565|gb|BJ964798.1|BJ964798
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|18344515|gb|BJ176556.1|BJ176556
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|162258931|gb|FC435874.1|FC435874
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCCAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|162230562|gb|FC407152.1|FC407152
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACCCCCAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|7207694|gb|AW561691.1|AW561691
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|208385764|gb|DC932708.1|DC932708
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|162216309|gb|FC392102.1|FC392102
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|208345545|gb|DC909235.1|DC909235
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|208351869|gb|DC913782.1|DC913782
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|18359133|gb|BJ191193.1|BJ191193
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|100352755|gb|BY945432.1|BY945432
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|208358888|gb|DC935218.1|DC935218
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|208357938|gb|DC938823.1|DC938823
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|162238217|gb|FC414303.1|FC414303
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|162233728|gb|FC409994.1|FC409994
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCCAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|208372029|gb|DC936229.1|DC936229
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAGGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|162201194|gb|FC377701.1|FC377701
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|162278464|gb|FC454550.1|FC454550
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCNAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|162169173|gb|FC345140.1|FC345140
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
EST: gi|208388058|gb|DC941697.1|DC941697
EST:     CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCT                         TCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT
genomic: CCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCT

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: 35 (upstream exon), 33 (downstream exon)
Score: 38

CTCAACATCGCCAACCCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgct ... ttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCTGGGAGATGAGTTTAAGGGGTATGTCTTCAAGATTATGGGAGGTTGCGAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggcagttgggaatcaaggttgcttcgcctttacacacacacacacttagcccgacagttctcttatcggtcgtcgatttcctttggtgtttgtgtttagTCGTCAATTCTACGACAAGAGACTGGCTCAGGAAGTTAGCGGTGACCAGCTGGGAGATGAGTTTAAGGGGTATGTCTTCAAGATTATGGGAGGTTGCGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG