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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgaatatagactttttactacattgatctttgtaactagacattcgaagcacccaatggtaaaccgaaagcattctttgacgtgaacacatctgtagaaccatatgactgacaattgccagtaccgtgaatgtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT

Basic information

species Physcomitrella patens
transcript PP1S243_27V6.5
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S243_27V6.5 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G18220.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttgaatatagactttttactacattgatctttgtaactagacattcgaagcacccaatggtaaaccgaaagcattctttgacgtgaacacatctgtagaaccatatgactgacaattgccagtaccgtgaatgtgatggcagCAATATGAT---AATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT
                                               ||    |    | |  | |  | |  |   || | || |  |       | |   ||   |  ||  |   | ||      |    ||| |  ||| ||| ||| | ||    ||| |  | | ||  | ||      |  |  |    | || |||||||  |||||||| ||||||||||||||||||||||
---------------------------------------------gtatgtacatt-tctatggatccatctcacttatacgttaatttcccggtttatcatgagggaattgtttcttattttgtgcaaatcggaaagaaatg-cagAAATTTCATCCGGATACTAAGGATGTTGTGTGTCATGGAGTTAAAAAGATAATCAAAGAAGGTTACAAGAGTTTCCCTAGTGGTCACACTTCAT
















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|100410611|gb|BY992184.1|BY992184
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|162269880|gb|FC445397.1|FC445397
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|100384546|gb|BY987405.1|BY987405
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACGCCCTC-AGCACTCAT
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACC-TCCAGCACTCAT
EST: gi|100426595|gb|BY977307.1|BY977307
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|208397735|gb|DC912532.1|DC912532
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCNGGAGTACTACTGCCATAGCT                         CAATATGATA-TATTGGGAACGTCATCTGCANAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|100354259|gb|BY945787.1|BY945787
EST:     CCGCCCTCACTTCTACNGCC-GTTGCTTCGGGAGTACTACTGCCATAGCT                         N
genomic: CCGCCCTCACTTCTAC-GCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcag-
EST: gi|100354259|gb|BY945787.1|BY945787
EST:     CCGCCCTCACTTCTACNGCC-GTTGCTTCGGGAGTACTACTGCCATAGCT                         N
genomic: CCGCCCTCACTTCTAC-GCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcag-
EST: gi|100407208|gb|BY974056.1|BY974056
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATGGGGGACGTCATCTGCAGAACA
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACA
EST: gi|100422036|gb|BY957830.1|BY957830
EST:     CCCGCCCTCACTTCTACGCC-GTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCA
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCA
EST: gi|100445033|gb|BY964332.1|BY964332
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|100354013|gb|BY983424.1|BY983424
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCTGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|208354965|gb|DC914229.1|DC914229
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|100411934|gb|BY992412.1|BY992412
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCNGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|162232054|gb|FC409128.1|FC409128
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|67571756|gb|BJ944580.1|BJ944580
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|100353507|gb|BY964841.1|BY964841
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|100420723|gb|BY993477.1|BY993477
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|208382440|gb|DC927974.1|DC927974
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
EST: gi|100413878|gb|BY975018.1|BY975018
EST:     CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCT                         CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG
genomic: CCCGCCCTCACTTCTACGCCCGTTGCTTCGGGAGTACTACTGCCATAGCTgtaagttgaa ... gtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatctgtagaaccatatgactgacaattgccagtaccgtgaatgtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT
                   gactgac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgaatatagactttttactacattgatctttgtaactagacattcgaagcacccaatggtaaaccgaaagcattctttgacgtgaacacatctgtagaaccatatgactgacaattgccagtaccgtgaatgtgatggcagCAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT