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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGACGGGATCCGGGCTGGGTTCTCTGTTGTTGGAGAGGTTGTCGGTGGACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatgcagatggcgatggcagagagtcaagttagggaggttgcgatgcgtgtggggagtgtggggataagaaggggatgtgtggcggcgagttgacggagtgggattgttgtggtggacag

Basic information

species Physcomitrella patens
transcript PP1S341_23V6.2
intron # 4
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|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|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|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|162159253|gb|FC335106.1|FC335106
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162174343|gb|FC350414.1|FC350414
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162179972|gb|FC356043.1|FC356043
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|162195647|gb|FC370310.1|FC370310
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
EST: gi|162219949|gb|FC396764.1|FC396764
EST:     ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAG                         GTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT
genomic: ACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGT

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: 33 (upstream exon), 35 (downstream exon)
Score: 101

CGGGACGGGATCCGGGCTGGGTTCTCTGTTGTTGGAGAGGTTGTCGGTGGACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatg ... tggtggacagGTGTCGACTGCAGTGGTGGAGCCATACAACAGCGTGCTGTCGACTCACAGTTTGTTGGAGCACACAGACGTGGCTGTGCTGTTGGACAATGAGGCAATTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGGACGGGATCCGGGCTGGGTTCTCTGTTGTTGGAGAGGTTGTCGGTGGACTACGGGAAGAAGTCGAAGCTGGGATTCACTATCTACCCGTCTCCCCAGgtatgcaatgcagatggcgatggcagagagtcaagttagggaggttgcgatgcgtgtggggagtgtggggataagaaggggatgtgtggcggcgagttgacggagtgggattgttgtggtggacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG