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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtccttcaaaatgttcggtaatgaccagatacaatcacgtgaatggcggtggatagtagtgctaatcttttttttctggtactggcgtgggttgttacagATGGTATTGTATGATACTCCAGGAGTGATTTCGAAGCAGGTTAAGAAGTTAGACGAGATGATGATGCGAAACGTTCGCACTGCCACCCTAAACGCAGATT

Basic information

species Physcomitrella patens
transcript PP1S399_34V6.1
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|100406192|gb|BY991585.1|BY991585
EST:     AGACAACTCGGCACCGCATCCTTGGGATTTGCTCCGGCCCTGATTATCAA                         ATGGTATTGTATGATACTCCAGGAGTGATTTCGAAGCAGGTTAAGAAGTTA
genomic: AGACAACTCGGCACCGCATCCTTGGGATTTGCTCCGGCCCTGATTATCAAgtacagataa ... gttgttacagATGGTATTGTATGATACTCCAGGAGTGATTTCGAAGCAGGTTAAGAAGTTA
EST: gi|100401437|gb|BY991002.1|BY991002
EST:     AGACAACTCGGCACCGCATCCTTGGGATTTGCTCCGGCCCTGATTATCAN                         ATGGTATTGTATGATACTCCAGGAGTGATTTCGAAGCAGGTAAAGAAGTTA
genomic: AGACAACTCGGCACCGCATCCTTGGGATTTGCTCCGGCCCTGATTATCAAgtacagataa ... gttgttacagATGGTATTGTATGATACTCCAGGAGTGATTTCGAAGCAGGTTAAGAAGTTA
EST: gi|100436617|gb|BY961307.1|BY961307
EST:     GACNACTCGGCACCGCATCCTTGGGATTTGCTCCGGCCCCTGAT-ATCAA                         ATGGTATTGTATGATACTC
genomic: GACAACTCGGCACCGCATCCTTGGGATTTGCTCCGGCCC-TGATTATCAAgtacagataa ... gttgttacagATGGTATTGTATGATACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcggtggatagtagtgctaatcttttttttctggtactggcgtgggttgttacagATGGTATTGTATGATACTCCAGGAGTGATTTCGAAGCAGGTTAAGAAGTTAGACGAGATGATGATGCGAAACGTTCGCACTGCCACCCTAAACGCAGATT
              tgctaat  putative branch site (score: 2)
                 taatcttttttttct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccttcaaaatgttcggtaatgaccagatacaatcacgtgaatggcggtggatagtagtgctaatcttttttttctggtactggcgtgggttgttacagATGGTATTGTATGATACTCCAGGAGTGATTTCGAAGCAGGTTAAGAAGTTAGACGAGATGATGATGCGAAACGTTCGCACTGCCACCCTAAACGCAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT