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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactccgattttacccttaaacctgtttgaaaatcacgggcaccttgtttattgacatgcttgatttctgcattattacctgtttcggtcgaagttttatgttcattatgattaaaatttccgcgcgtggtgcttgctctgctccattggcag

Basic information

species Physcomitrella patens
transcript PP1S32_313V6.1
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|19785989|gb|BQ040423.1|BQ040423
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCANGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTTGA-CAAGGAAATCCCTCT
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTT-GAACAAGGAAATCCCTCT
EST: gi|162169717|gb|FC345254.1|FC345254
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|208364552|gb|DC930942.1|DC930942
EST:     TAAATGTTGANGGCCTGCGTGGTTTTGTGCCTTTCTCTCANGTTTCAGCT                         AGGGGTGCCCAGTCC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCC
EST: gi|162249173|gb|FC420398.1|FC420398
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAACT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|162189197|gb|FC366719.1|FC366719
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|162156033|gb|FC332200.1|FC332200
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|162252958|gb|FC429019.1|FC429019
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|162174660|gb|FC351348.1|FC351348
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|18327036|gb|BJ159037.1|BJ159037
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|162196282|gb|FC375391.1|FC375391
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|162167953|gb|FC344891.1|FC344891
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AAGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|208396404|gb|DC920070.1|DC920070
EST:     TAGATGNTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|162223594|gb|FC399718.1|FC399718
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|162187440|gb|FC362662.1|FC362662
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|208380465|gb|DC914889.1|DC914889
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGA
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGA
EST: gi|162263938|gb|FC439207.1|FC439207
EST:     CAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: CAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|162223593|gb|FC399717.1|FC399717
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|208365201|gb|DC931167.1|DC931167
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|162263939|gb|FC439208.1|FC439208
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|208392949|gb|DC928635.1|DC928635
EST:     CTCTCAGG-TTCAGCT                         A-GGGTGCCCAGTCCAACCCTGAAGAAC-TTTGAACAAGGAAATCCCTCTC
genomic: CTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|208389104|gb|DC945680.1|DC945680
EST:     TAGATGTTGAGGGCCTGCGTGNTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTC
EST: gi|100387097|gb|BY951496.1|BY951496
EST:     TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT                         AGGGGTGCCCAGTCCAAC
genomic: TAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAAC

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), 29 (downstream exon)
Score: 17

ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactc ... ccattggcagAGGGGTGCCCAGTCCAACCCTGAAGAACTTTTGAACAAGGAAATCCCTCTCAAGTTCCTCGAGGTTGATGAGGAGCGCACGCGTCTTGTTCTTAGCAACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCTgtaagtactccgattttacccttaaacctgtttgaaaatcacgggcaccttgtttattgacatgcttgatttctgcattattacctgtttcggtcgaagttttatgttcattatgattaaaatttccgcgcgtggtgcttgctctgctccattggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT