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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactgtacgatcttatggaagtgtgcgtgacttcgatattactcgaattgatcatgtttttttgagaaagtccagactgatttgacttgtacgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG

Basic information

species Physcomitrella patens
transcript PP1S172_22V6.1
intron # 2
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|100443039|gb|BY981665.1|BY981665
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|208376452|gb|DC902749.1|DC902749
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|67717448|gb|BJ967707.1|BJ967707
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|208389492|gb|DC942199.1|DC942199
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|100369785|gb|BY967385.1|BY967385
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|162174625|gb|FC350280.1|FC350280
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|18347384|gb|BJ179430.1|BJ179430
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|18356387|gb|BJ188446.1|BJ188446
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|67718156|gb|BJ968415.1|BJ968415
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|67704223|gb|BJ964456.1|BJ964456
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|18369160|gb|BJ201245.1|BJ201245
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|100353391|gb|BY964783.1|BY964783
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|67716670|gb|BJ966930.1|BJ966930
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|208390428|gb|DC933685.1|DC933685
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|67717265|gb|BJ967524.1|BJ967524
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|100355882|gb|BY946086.1|BY946086
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|67712935|gb|BJ966384.1|BJ966384
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|162229414|gb|FC405605.1|FC405605
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|100383611|gb|BY969140.1|BY969140
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGAAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|18366975|gb|BJ199055.1|BJ199055
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|18346613|gb|BJ178658.1|BJ178658
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|18354799|gb|BJ186857.1|BJ186857
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|208367162|gb|DC935962.1|DC935962
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|18341969|gb|BJ174004.1|BJ174004
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|18356942|gb|BJ189001.1|BJ189001
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|67571497|gb|BJ944321.1|BJ944321
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|100363442|gb|BY966391.1|BY966391
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|18372682|gb|BJ204284.1|BJ204284
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|67703235|gb|BJ963468.1|BJ963468
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGGGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|67717486|gb|BJ967745.1|BJ967745
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|67569243|gb|BJ942067.1|BJ942067
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|18364140|gb|BJ196213.1|BJ196213
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|100415505|gb|BY992875.1|BY992875
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|100360303|gb|BY966108.1|BY966108
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
EST: gi|100427995|gb|BY959230.1|BY959230
EST:     GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAG                         GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT
genomic: GGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATT

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), 29 (downstream exon)
Score: 11

TGCCGCCGAGTATGTGGGCGTCAAGATTGAATTCACCGAGATAACGGACTGGTCCACTACCAAGTCTCCCCAGTACCTTGCGATGAATCCCATGGGAAAGgtatgctgtt ... acgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgatcatgtttttttgagaaagtccagactgatttgacttgtacgtctgcagGTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG
        atgttttttt  TA-rich tract