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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgactgctagtgatttttatggctggcgtcctagtttttagttgtgaagtttcaacaagtgacattttcttagttacttacatcagaaacagataattccttgggcagaacatctttaaataattcttacggtctgcaaaagatgtgttatctctgacctcatgtcaacaattttggatttgtcaatag

Basic information

species Physcomitrella patens
transcript PP1S165_119V6.2
intron # 3
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|100439869|gb|BY980280.1|BY980280
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|208360006|gb|DC939310.1|DC939310
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|18351813|gb|BJ183865.1|BJ183865
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAACCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAA
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAA
EST: gi|18373505|gb|BJ205083.1|BJ205083
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|100447198|gb|CJ971497.1|CJ971497
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|67709495|gb|BJ965311.1|BJ965311
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|100397857|gb|BY990436.1|BY990436
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|100422751|gb|BY957982.1|BY957982
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|100386905|gb|BY988174.1|BY988174
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|100401634|gb|BY954629.1|BY954629
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|100436225|gb|BY979442.1|BY979442
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|100360406|gb|BY984111.1|BY984111
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAANAAAAAG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|18367245|gb|BJ199326.1|BJ199326
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGA
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGA
EST: gi|100422530|gb|BY976419.1|BY976419
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGGCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|100390752|gb|BY971507.1|BY971507
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNN-G                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
EST: gi|67574586|gb|BJ947410.1|BJ947410
EST:     ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGNNNNNNNNG                         ATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT
genomic: ATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATT

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: 26 (upstream exon), 25 (downstream exon)
Score: 9

GGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgact ... ttgtcaatagATCAAAAGAGAGATCAAGATTCTGCAAAACCTTTGTGGAGGGCCCAACATTGTGAAGCTTCTGGACATTGTCCGTGATCAGCAATCGAAGACACCCAGCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGGGCGAGGGAAATACAGTGAGGTTTTTGAAGGTGTCAACGCCGTGAATAGTGAGCGTTGCGTTATGAAGATTTTGAAGCCAGTAAAGAAAAAAAAGgtacctgactgctagtgatttttatggctggcgtcctagtttttagttgtgaagtttcaacaagtgacattttcttagttacttacatcagaaacagataattccttgggcagaacatctttaaataattcttacggtctgcaaaagatgtgttatctctgacctcatgtcaacaattttggatttgtcaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA