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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gctggtatcagatcgccagtagccaaacagtcttctctatatcatttctgagcttaaagatgtcgttgcagtctcaattgtgcgtggcaaccatttctgtccacagaggctaacactgatcgagtttctattgcggagcagGCTGTGGAGCGGCACTAGAAGTGAGAGGGGGAGGAAGGGCTTGTTGAGTGCTCGGATTTCGGGAGCAAACCATGGCAAAAGACGTGGGCGTGGAGCCTGG

Basic information

species Physcomitrella patens
transcript PP1S55_301V6.2
intron # 1
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|100441269|gb|BY962558.1|BY962558
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100441269|gb|BY962558.1|BY962558
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100367803|gb|BY984790.1|BY984790
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100367803|gb|BY984790.1|BY984790
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100444954|gb|BY982782.1|BY982782
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100444954|gb|BY982782.1|BY982782
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100444954|gb|BY982782.1|BY982782
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100444954|gb|BY982782.1|BY982782
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100444954|gb|BY982782.1|BY982782
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100444954|gb|BY982782.1|BY982782
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100444954|gb|BY982782.1|BY982782
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18327139|gb|BJ159140.1|BJ159140
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18327139|gb|BJ159140.1|BJ159140
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18363932|gb|BJ196004.1|BJ196004
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTTTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18363932|gb|BJ196004.1|BJ196004
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTTTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100446330|gb|CJ970629.1|CJ970629
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100446330|gb|CJ970629.1|CJ970629
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100450809|gb|CJ974450.1|CJ974450
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100450809|gb|CJ974450.1|CJ974450
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100385719|gb|BY987784.1|BY987784
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100385719|gb|BY987784.1|BY987784
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100450101|gb|CJ974094.1|CJ974094
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100450101|gb|CJ974094.1|CJ974094
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18326909|gb|BJ158909.1|BJ158909
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18326909|gb|BJ158909.1|BJ158909
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|208391222|gb|DC933511.1|DC933511
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|208391222|gb|DC933511.1|DC933511
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100416508|gb|BY975423.1|BY975423
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100416508|gb|BY975423.1|BY975423
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100436853|gb|BY979558.1|BY979558
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100436853|gb|BY979558.1|BY979558
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100441166|gb|BY980787.1|BY980787
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100441166|gb|BY980787.1|BY980787
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|162181259|gb|FC357041.1|FC357041
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|162181259|gb|FC357041.1|FC357041
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100438936|gb|BY961878.1|BY961878
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100438936|gb|BY961878.1|BY961878
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18359721|gb|BJ191782.1|BJ191782
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGT                         GCTGGCTGCGGAGCGGCACTAGAAGTGAGAGGGGGAGGAAGGGCTTGTTGA
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTgctggtatca ... tgcggagcagGCT-G-T--GGAGCGGCACTAGAAGTGAGAGGGGGAGGAAGGGCTTGTTGA
EST: gi|162181095|gb|FC357267.1|FC357267
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|162181095|gb|FC357267.1|FC357267
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18372638|gb|BJ204240.1|BJ204240
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18372638|gb|BJ204240.1|BJ204240
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100356719|gb|BY965246.1|BY965246
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100356719|gb|BY965246.1|BY965246
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|162246016|gb|FC424388.1|FC424388
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|162246016|gb|FC424388.1|FC424388
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100448690|gb|CJ972989.1|CJ972989
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|100448690|gb|CJ972989.1|CJ972989
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18365833|gb|BJ197911.1|BJ197911
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc
EST: gi|18365833|gb|BJ197911.1|BJ197911
EST:     AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACAGTGCT                       
genomic: AGTTAGCGCATTAACTTCCGCAGCATCGCCCATTCTTTAAGATCCACA--G-Tgctggtatca ... tgcggagc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaccatttctgtccacagaggctaacactgatcgagtttctattgcggagcagGCTGTGGAGCGGCACTAGAAGTGAGAGGGGGAGGAAGGGCTTGTTGAGTGCTCGGATTTCGGGAGCAAACCATGGCAAAAGACGTGGGCGTGGAGCCTGG
                                      tttctatt  CT-rich tract
                                      tttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctggtatcagatcgccagtagccaaacagtcttctctatatcatttctgagcttaaagatgtcgttgcagtctcaattgtgcgtggcaaccatttctgtccacagaggctaacactgatcgagtttctattgcggagcagGCTGTGGAGCGGCACTAGAAGTGAGAGGGGGAGGAAGGGCTTGTTGAGTGCTCGGATTTCGGGAGCAAACCATGGCAAAAGACGTGGGCGTGGAGCCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG