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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgcagaaatattcacttcgtagtctctgtgcaagatagcaaacgatcatcctattcttgatgcatactaaagaaagaatatttgaatggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCGAACGAAGGGCAGGGTCTGGGCAATGCCTTTTTGTCACATATTCGAGCGG

Basic information

species Physcomitrella patens
transcript PP1S207_28V6.1
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|18361521|gb|BJ193587.1|BJ193587
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|162272681|gb|FC448307.1|FC448307
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|208383342|gb|DC907517.1|DC907517
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|67573864|gb|BJ946688.1|BJ946688
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|18363393|gb|BJ195465.1|BJ195465
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|100415938|gb|BY956998.1|BY956998
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|208370398|gb|DC931810.1|DC931810
EST:     CTAATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|208394358|gb|DC904178.1|DC904178
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|100451884|gb|CJ974990.1|CJ974990
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|100395348|gb|BY953692.1|BY953692
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|162263698|gb|FC439623.1|FC439623
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|18358448|gb|BJ190507.1|BJ190507
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|162202372|gb|FC379991.1|FC379991
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|100387386|gb|BY988257.1|BY988257
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|208399872|gb|DC904954.1|DC904954
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|162264593|gb|FC440889.1|FC440889
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|18361750|gb|BJ193817.1|BJ193817
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTTCGCGGTGC
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTT-CGCGGTGC
EST: gi|18347703|gb|BJ179750.1|BJ179750
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|208397168|gb|DC911777.1|DC911777
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|100352204|gb|BY983091.1|BY983091
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|208391589|gb|DC933838.1|DC933838
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|162278437|gb|FC454523.1|FC454523
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|18351948|gb|BJ184000.1|BJ184000
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|18363198|gb|BJ195270.1|BJ195270
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|18347772|gb|BJ179819.1|BJ179819
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|208393061|gb|DC929556.1|DC929556
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|18345717|gb|BJ177760.1|BJ177760
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCCTGGTTTTAGTTCGCGGTG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGC-TGGTTT-AGTTCGCGGTG
EST: gi|162175835|gb|FC352137.1|FC352137
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|18371439|gb|BJ203041.1|BJ203041
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|18347497|gb|BJ179543.1|BJ179543
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|208359117|gb|DC930449.1|DC930449
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|18349457|gb|BJ181506.1|BJ181506
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
EST: gi|100386335|gb|BY988002.1|BY988002
EST:     CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAG                         GTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG
genomic: CTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 30 (upstream exon), 34 (downstream exon)
Score: 13

GAATTTTCCTTTCTGTACAATTGAGCCCAATGAAGCACGCGTTTACGTACCTGATGAGAGGTTCGATTGGCTCTGCCAGCTGTTCAAACCGAAAAGCGAGgttatttacg ... ggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCGAACGAAGGGCAGGGTCTGGGCAATGCCTTTTTGTCACATATTCGAGCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatcatcctattcttgatgcatactaaagaaagaatatttgaatggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCGAACGAAGGGCAGGGTCTGGGCAATGCCTTTTTGTCACATATTCGAGCGG
                      tactaaa  putative branch site (score: 13)
                         taaagaaagaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgcagaaatattcacttcgtagtctctgtgcaagatagcaaacgatcatcctattcttgatgcatactaaagaaagaatatttgaatggtgaaccagGTGGCCGCTTTTCTTGAGATTAACGACATCGCTGGTTTAGTTCGCGGTGCGAACGAAGGGCAGGGTCTGGGCAATGCCTTTTTGTCACATATTCGAGCGG

tgctgca