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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtagtgtttcttgacatctgcattctacacctattttctattggtatttatttgtcttcagcatgtaatttgcgctctcgtgctgctaatttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCATGAACTGCTTCAGCCCTACCCTGTTCTTCACGAAAAGCCCG

Basic information

species Physcomitrella patens
transcript PP1S264_34V6.1
intron # 6
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|208386880|gb|DC956891.1|DC956891
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|67726166|gb|BJ976425.1|BJ976425
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|37836413|gb|BJ594421.1|BJ594421
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|67720297|gb|BJ970556.1|BJ970556
EST:     TATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: TATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|37827952|gb|BJ585964.1|BJ585964
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|67693669|gb|BJ953902.1|BJ953902
EST:     AATCAATACCAAGTTCCCTATTATGCCTTNCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: AATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|162162327|gb|FC338304.1|FC338304
EST:     CAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: CAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|162206837|gb|FC382699.1|FC382699
EST:     ATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|162241037|gb|FC416668.1|FC416668
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|162255462|gb|FC431876.1|FC431876
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|162180761|gb|FC357846.1|FC357846
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|162236928|gb|FC412879.1|FC412879
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|162236927|gb|FC412878.1|FC412878
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|162180762|gb|FC357847.1|FC357847
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|67697855|gb|BJ958088.1|BJ958088
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|18335638|gb|BJ167658.1|BJ167658
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
EST: gi|162206838|gb|FC382700.1|FC382700
EST:     ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAG                         AGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA
genomic: ATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCA

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), 30 (downstream exon)
Score: 10

AGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAATCAATACCAAGTTCCCTATTATGCCTTTCACTGCTAGgtactgcttt ... atttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCATGAACTGCTTCAGCCCTACCCTGTTCTTCACGAAAAGCCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttatttgtcttcagcatgtaatttgcgctctcgtgctgctaatttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCATGAACTGCTTCAGCCCTACCCTGTTCTTCACGAAAAGCCCG
                                        tgctaat  putative branch site (score: 10)
                                              tttattc  CT-rich tract
                                           taatttattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtagtgtttcttgacatctgcattctacacctattttctattggtatttatttgtcttcagcatgtaatttgcgctctcgtgctgctaatttattcagAGCTCTAGAAGAGAAGAGGGCCCGCCTTGGTATCGTGGAGTGTGTTAACCATGAACTGCTTCAGCCCTACCCTGTTCTTCACGAAAAGCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgct