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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGAAGAACGGCCGGGACGACGAAGATCTCCTTCTGTGGTTTCTTCGTGATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcctaatctaaaatatgctgatctatgaacaccacctcatgttccttattgacctaccctaatcttcacttccaatttgtacgaatacttgaat...

Basic information

species Physcomitrella patens
transcript PP1S4_80V6.1
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|208345072|gb|DC925426.1|DC925426
EST:     TCGAAAG-TTGACGTTGACGCAGCTGTGGAGAAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: TCGAAAGTTTGACGTTGACGCAGCTGTGGAG-AAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|100432131|gb|BY960350.1|BY960350
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTTCTATA-G
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATT-CTATAAG
EST: gi|208379403|gb|DC919019.1|DC919019
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|162279530|gb|FC455321.1|FC455321
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|208379109|gb|DC911634.1|DC911634
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|208399395|gb|DC924825.1|DC924825
EST:     ATCGAAAGNTNGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|162279529|gb|FC455320.1|FC455320
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|208344682|gb|DC905131.1|DC905131
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|37838301|gb|BJ596309.1|BJ596309
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|208376190|gb|DC911014.1|DC911014
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|162258991|gb|FC435934.1|FC435934
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGAAGAACGGCCGGGACGACGAAGATCTCCTTCTGTGGTTTCTTCGTGATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcctaatctaaaatatgctgatctatgaacaccacctcatgttccttattgacctaccctaatcttcacttccaatttgtacgaatacttgaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA