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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaatgcagatggcgatggcagagagtcaagttagggaggttgcgatgcgtgtggggagtgtggggataagaaggggatgtgtggcggcgagttgacggagtgggattgttgtggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGTTTGTTGGAGCACACAGACGTGGCTGTGCTGTTGGACAATGAGGCAATTT

Basic information

species Physcomitrella patens
transcript PP1S341_23V6.1
intron # 3
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|100401155|gb|BY990858.1|BY990858
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162167933|gb|FC344871.1|FC344871
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162169581|gb|FC346145.1|FC346145
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162215756|gb|FC390821.1|FC390821
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162187183|gb|FC363693.1|FC363693
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|100447498|gb|CJ971797.1|CJ971797
EST:     ACTACGGGAAGAAGTCNAAGCTGGGATTCACTATCTACCCGTCTCCC-AG                         GTGTCGACTGCAGTGGTGGANCNATACAACAGCGTGCTGTC
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTC
EST: gi|208398501|gb|DC912374.1|DC912374
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162153183|gb|FC329589.1|FC329589
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|208367360|gb|DC939876.1|DC939876
EST:     ACTACNGGAANAANTCNAANCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCA-TGGTGNA-CCATACAACAGCGTGCTGTCGACTCAC
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCAC
EST: gi|100416761|gb|BY993074.1|BY993074
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162197748|gb|FC374998.1|FC374998
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162264420|gb|FC440586.1|FC440586
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162155722|gb|FC331335.1|FC331335
EST:     CGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: CGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162171365|gb|FC347264.1|FC347264
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162229157|gb|FC404516.1|FC404516
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162186501|gb|FC363265.1|FC363265
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162219666|gb|FC395662.1|FC395662
EST:     CTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: CTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|100378281|gb|BY949772.1|BY949772
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCCATACA-CAGCGTGCTGTCGACTCACAG
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCC-ATACAACAGCGTGCTGTCGACTCACAG
EST: gi|162159253|gb|FC335106.1|FC335106
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|100398871|gb|BY990557.1|BY990557
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAACGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|208361994|gb|DC943463.1|DC943463
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162174343|gb|FC350414.1|FC350414
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|208364662|gb|DC939429.1|DC939429
EST:     ACTACNGGAAGAANTCGAANCTGGGATNCACTATCTACCCGTCTCCC-AG                         GTGTCGACTGCAGTG
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTG
EST: gi|67573333|gb|BJ946157.1|BJ946157
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGT
EST: gi|162179972|gb|FC356043.1|FC356043
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|100367015|gb|BY948325.1|BY948325
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|208373771|gb|DC936570.1|DC936570
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162189300|gb|FC366770.1|FC366770
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162162283|gb|FC338065.1|FC338065
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162170569|gb|FC347689.1|FC347689
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATAC
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATAC
EST: gi|208345518|gb|DC909208.1|DC909208
EST:     ACTACNGGAAGAANCCGAAGCTGGNATTCACTATCTACCNGTCTCCCCAN                         GTGTCGACTGCA-TGGTGNANC-ATACAACANCNTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162195647|gb|FC370310.1|FC370310
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|100411792|gb|BY992343.1|BY992343
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162219949|gb|FC396764.1|FC396764
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagaaggggatgtgtggcggcgagttgacggagtgggattgttgtggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGTTTGTTGGAGCACACAGACGTGGCTGTGCTGTTGGACAATGAGGCAATTT
                       agttgac  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaatgcagatggcgatggcagagagtcaagttagggaggttgcgatgcgtgtggggagtgtggggataagaaggggatgtgtggcggcgagttgacggagtgggattgttgtggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGTTTGTTGGAGCACACAGACGTGGCTGTGCTGTTGGACAATGAGGCAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT