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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgccttgctccgaacgatccttgaatcttccagccatcagtcccggttacgatttcacgtgagactgcgtctggtgcgtttcagagctgttgtgaccatctttctgatcactgtacgttttgcggatcttcag

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S243_27V6.5 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT3G18220.1 (Arabidopsis thaliana), 5'ss of exon 5
CAATATGAT---AATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgccttgctccgaacgatccttgaatcttccagc--catcagtcccggttacgatttcacgtgagactgcgtctggtgcgtttcagagctgttgtgaccatctttctgatcactgtacgttttgcggatcttcag
 ||| | ||    ||| |  | | ||  | ||      |  |  |    | || |||||||  |||||||| |||||||||||||||||||||||| |||    || ||  ||  ||     |  |    | |  |||| |    | || || ||| | || | || || |    | || |  | |  ||  |                                         
AAATTTCATCCGGATACTAAGGATGTTGTGTGTCATGGAGTTAAAAAGATAATCAAAGAAGGTTACAAGAGTTTCCCTAGTGGTCACACTTCATgtaagt----tgttctaaagcattaaaaagacaagtaacaacatctgaattgattccggttt-atgtta-accgc-ttgattacggtataca--tgcag-----------------------------------------
















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|162269879|gb|FC445396.1|FC445396
EST:     AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT                         GGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
genomic: AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgcct ... ggatcttcagGGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
EST: gi|100410611|gb|BY992184.1|BY992184
EST:     AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT                         GGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
genomic: AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgcct ... ggatcttcagGGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
EST: gi|162269880|gb|FC445397.1|FC445397
EST:     AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT                         GGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
genomic: AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgcct ... ggatcttcagGGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
EST: gi|162232053|gb|FC409127.1|FC409127
EST:     AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT                         GGTCTTTCGCAGGTTTGGGGTACTNGTCGATGTATTTGGCTGGCAAGCTCG
genomic: AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgcct ... ggatcttcagGGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
EST: gi|208354965|gb|DC914229.1|DC914229
EST:     AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT                         GGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
genomic: AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgcct ... ggatcttcagGGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
EST: gi|100411934|gb|BY992412.1|BY992412
EST:     NGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT                         GGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
genomic: AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgcct ... ggatcttcagGGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
EST: gi|162232054|gb|FC409128.1|FC409128
EST:     AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT                         GGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
genomic: AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgcct ... ggatcttcagGGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
EST: gi|100420723|gb|BY993477.1|BY993477
EST:     AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT                         GGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
genomic: AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgcct ... ggatcttcagGGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
EST: gi|208382440|gb|DC927974.1|DC927974
EST:     AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCAT                         GGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG
genomic: AGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgcct ... ggatcttcagGGTCTTTCGCAGGTTTGGGGTACTTGTCGATGTATTTGGCTGGCAAGCTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATATGATAATATTGGGAACGTCATCTGCAGAACACCTCCAGCACTCATGAAAGAAGCATACAAGAGCTTCCCTAGTGGTCACACTTCATgtgagtgccttgctccgaacgatccttgaatcttccagccatcagtcccggttacgatttcacgtgagactgcgtctggtgcgtttcagagctgttgtgaccatctttctgatcactgtacgttttgcggatcttcag

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