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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaaacaggaaattgtagcttctaaaatcgcagctttggacccgattagagaattccgcactctagtgcccttagcatttccgttttcctttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGAGGCAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTT

Basic information

species Physcomitrella patens
transcript PP1S205_25V6.1
intron # 7
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|208371212|gb|DC956004.1|DC956004
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|67724192|gb|BJ974451.1|BJ974451
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162170103|gb|FC347015.1|FC347015
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162177265|gb|FC353422.1|FC353422
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162179280|gb|FC356229.1|FC356229
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|208359054|gb|DC957802.1|DC957802
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|208354342|gb|DC953790.1|DC953790
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162179279|gb|FC356228.1|FC356228
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162227183|gb|FC402826.1|FC402826
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|37832669|gb|BJ590681.1|BJ590681
EST:     CCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162159392|gb|FC334660.1|FC334660
EST:     GAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: GAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|208357076|gb|DC926507.1|DC926507
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162178856|gb|FC354788.1|FC354788
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162167604|gb|FC344256.1|FC344256
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|208347204|gb|DC949745.1|DC949745
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|37840478|gb|BJ598486.1|BJ598486
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162203866|gb|FC379963.1|FC379963
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162181031|gb|FC358685.1|FC358685
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162167605|gb|FC344257.1|FC344257
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162278585|gb|FC454047.1|FC454047
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162203867|gb|FC379964.1|FC379964
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|208361679|gb|DC954127.1|DC954127
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162153878|gb|FC330009.1|FC330009
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162179456|gb|FC355456.1|FC355456
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162187678|gb|FC364629.1|FC364629
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162177062|gb|FC353115.1|FC353115
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|208381579|gb|DC915445.1|DC915445
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|37836121|gb|BJ594129.1|BJ594129
EST:     TGAAGGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGNAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGG
genomic: TGAA-GGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGG-AAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGG
EST: gi|208360740|gb|DC946464.1|DC946464
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162177266|gb|FC353423.1|FC353423
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162179457|gb|FC355457.1|FC355457
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTG
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTG
EST: gi|162170104|gb|FC347016.1|FC347016
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|67698740|gb|BJ958973.1|BJ958973
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
EST: gi|162227182|gb|FC402825.1|FC402825
EST:     CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAA                         GTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA
genomic: CGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGA

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: 30 (upstream exon), 35 (downstream exon)
Score: 18

CTCACCCCACTCCCACACGAGCAGAGGTTTCAGACATAGCTATTGCCGTCCGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacct ... tttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGAGGCAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagagaattccgcactctagtgcccttagcatttccgttttcctttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGAGGCAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTT
                               catttccgttttcctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaaacaggaaattgtagcttctaaaatcgcagctttggacccgattagagaattccgcactctagtgcccttagcatttccgttttcctttggattagGTATCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGAGGCAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG