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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcccacagttatttttaaagttagattttgctctaatggcatgagcatcgtataatggaaccttgttctcttttctatttctgcacag

Basic information

species Physcomitrella patens
transcript PP1S79_254V6.2
intron # 4
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|100398771|gb|BY990507.1|BY990507
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|100398308|gb|BY972539.1|BY972539
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|208395729|gb|DC911822.1|DC911822
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|18372904|gb|BJ204506.1|BJ204506
EST:     CATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: CATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGG-AGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|18358733|gb|BJ190792.1|BJ190792
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAA
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAA
EST: gi|100404436|gb|BY973577.1|BY973577
EST:     CATCGACCACGAGCTGTTCTTTCAGTGAACATTGGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGGACATTGGGCCTTCTTGGGTCTCGAATCGTAC
genomic: CATCGACCACGAGCTGTTCTTTCAGTGAACATTGG-TGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGG-TCTCGAATCGTAC
EST: gi|208346919|gb|DC905449.1|DC905449
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAATGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|208400165|gb|DC904813.1|DC904813
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|18352604|gb|BJ184658.1|BJ184658
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAAC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAAC
EST: gi|18343422|gb|BJ175460.1|BJ175460
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCANTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|208350210|gb|DC901594.1|DC901594
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|100363297|gb|BY984455.1|BY984455
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|100437331|gb|BY961467.1|BY961467
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGA-CATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|208398960|gb|DC912119.1|DC912119
EST:     TCATCGACCACGAGCTGTTCTTTCANTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|100439349|gb|BY980219.1|BY980219
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAANGAACATTGGGCCTTTCT-GGTCTCGAATCGTAC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTT-CTTGGTCTCGAATCGTAC
EST: gi|208391691|gb|DC942281.1|DC942281
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|100353619|gb|BY964897.1|BY964897
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|18354389|gb|BJ186445.1|BJ186445
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|208378690|gb|DC914664.1|DC914664
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
EST: gi|18356417|gb|BJ188476.1|BJ188476
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAA
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAA
EST: gi|100432416|gb|BY960464.1|BY960464
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAAGGA-CATTGGGCCTTCTTGGTCTCGAATCGTAC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAA-GGAACATTGGGCCTTCTTGGTCTCGAATCGTAC
EST: gi|100408155|gb|BY955925.1|BY955925
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGGACATTGGTGGAGTTGACTTTG                         ATGGCA-TCAGTAACGAAGGAACATTGGGGCTTTCTGGGTCTCGAATCGTA
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATG-CAATCAGTAACGAAGGAACATTGGGCCTT-CTTGGTCTCGAATCGTA
EST: gi|100413319|gb|BY956613.1|BY956613
EST:     TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTG                         ATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC
genomic: TCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACC

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: 16 (upstream exon), 29 (downstream exon)
Score: 8

ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcc ... ttctgcacagATGCAATCAGTAACGAAGGAACATTGGGCCTTCTTGGTCTCGAATCGTACCAGCTTCGTCCTTTGATTGCAGAAGACGCGCACTTCCGACAAACGATTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGATTCTGTGGTGACACCTAATCCATTTCATCGACCACGAGCTGTTCTTTCAGTGAACATTGGTGGAGTTGACTTTGgtaagtatcccacagttatttttaaagttagattttgctctaatggcatgagcatcgtataatggaaccttgttctcttttctatttctgcacag

- - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG