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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTAGTGTCGAGTCGCATTTGACTAGCCGGCGACAGCTTCTCCTTCTCGTGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctcttttggcggtagttctatatcattcatgcttttgcgcttcgggcttaatgcgtgcactatttaaatcttatattagcccgatccttctca...

Basic information

species Physcomitrella patens
transcript PP1S396_19V6.1
intron # 1
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|100423813|gb|BY976549.1|BY976549
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|208382420|gb|DC927954.1|DC927954
EST:     GTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGNTGACACAACAATTACGGATCGTGTCTACCTT
genomic: GTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|208375329|gb|DC936956.1|DC936956
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|100383637|gb|BY969166.1|BY969166
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|208389670|gb|DC938274.1|DC938274
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|208354944|gb|DC914208.1|DC914208
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|100398209|gb|BY954143.1|BY954143
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|162171130|gb|FC347744.1|FC347744
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|208385133|gb|DC911379.1|DC911379
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|208387283|gb|DC933034.1|DC933034
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|162168541|gb|FC344465.1|FC344465
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|100430768|gb|BY978387.1|BY978387
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|208344474|gb|DC905035.1|DC905035
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|67572290|gb|BJ945114.1|BJ945114
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|208398169|gb|DC908398.1|DC908398
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|67573286|gb|BJ946110.1|BJ946110
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|208349913|gb|DC913621.1|DC913621
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|162258735|gb|FC434534.1|FC434534
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
EST: gi|162254581|gb|FC429431.1|FC429431
EST:     TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAG                         GAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT
genomic: TGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTT

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-Seq library.


Block sizes: 33 (upstream exon), 35 (downstream exon)
Score: 9

ATGTAGTGTCGAGTCGCATTTGACTAGCCGGCGACAGCTTCTCCTTCTCGTGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctc ... ctggtcgcagGAGACTGGCACATCGGGTGTTGACACAACAATTACGGATCGTGTCTACCTTGATATTATGGAATGTCCTAGCTTAGCGAGGGCCGATCGAACTCTTGGCA





























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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTAGTGTCGAGTCGCATTTGACTAGCCGGCGACAGCTTCTCCTTCTCGTGTCCGGCGCGGCTGTGACTGCAGCTGCTTTGCCTTCTTACGCTGATGAGgtatcgtctcttttggcggtagttctatatcattcatgcttttgcgcttcgggcttaatgcgtgcactatttaaatcttatattagcccgatccttctca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT