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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACGTTACCAATTTCAACAAGGCTTTGGAGCAGATGCACTCCTCCAATGATCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggttagaacctggagtttaggtttgtgtatttattttttcctttttttttttttttttttttttttttttctctgattttggaggggaatcggcttgcgtgggtttatgtttctttttttgtttttttgggggggtttgtgctgcag

Basic information

species Physcomitrella patens
transcript PP1S174_60V6.1
intron # 1
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|162260962|gb|FC438019.1|FC438019
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|208366209|gb|DC955308.1|DC955308
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|162235362|gb|FC412329.1|FC412329
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|7147644|gb|AW509566.1|AW509566
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|208391751|gb|DC942313.1|DC942313
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|208397933|gb|DC916688.1|DC916688
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|18346645|gb|BJ178690.1|BJ178690
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACC
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACC
EST: gi|208348700|gb|DC926375.1|DC926375
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|208344646|gb|DC912592.1|DC912592
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|37834392|gb|BJ592404.1|BJ592404
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|37831305|gb|BJ589317.1|BJ589317
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|18351976|gb|BJ184028.1|BJ184028
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|100441642|gb|BY962733.1|BY962733
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|6102404|gb|AW126874.1|AW126874
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|208377497|gb|DC902792.1|DC902792
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
EST: gi|162235361|gb|FC412328.1|FC412328
EST:     TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAG                         GGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT
genomic: TCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT

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), 35 (downstream exon)
Score: 57

TACGTTACCAATTTCAACAAGGCTTTGGAGCAGATGCACTCCTCCAATGATCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggtt ... tgtgctgcagGGCATGTTAATCACTCAATCTTTTGGAAGAATCTTGCACCCATCAGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACGTTACCAATTTCAACAAGGCTTTGGAGCAGATGCACTCCTCCAATGATCCACAGACCATTGTTGCCCTGCAGTCCGCTATCAATTTCAATGGCGGAGgtacgtggttagaacctggagtttaggtttgtgtatttattttttcctttttttttttttttttttttttttttttctctgattttggaggggaatcggcttgcgtgggtttatgtttctttttttgtttttttgggggggtttgtgctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG