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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTTCAAGAAGGACAACAGCGAGAAGAAGCTGAACTTGGGAGTAGGTGCTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaatatctgcttggcaatgtaccacataccatccttcagaaagtgccactgattcaagtcgtctcaaatacagcttctcctattgtgccacttttgctctctgagcgaagcattaaccatcaggctcaggagtgtttagaaggtatctgattctttcaatctttacag

Basic information

species Physcomitrella patens
transcript PP1S540_7V6.2
intron # 3
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|208372110|gb|DC940292.1|DC940292
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|67574849|gb|BJ947673.1|BJ947673
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|18374954|gb|BJ206532.1|BJ206532
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|100359406|gb|BY984238.1|BY984238
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|67570023|gb|BJ942847.1|BJ942847
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|100369975|gb|BY967466.1|BY967466
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|18366753|gb|BJ198832.1|BJ198832
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGGGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|100397833|gb|BY990424.1|BY990424
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|162172938|gb|FC348943.1|FC348943
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|208359935|gb|DC938956.1|DC938956
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|162167595|gb|FC343740.1|FC343740
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|18358325|gb|BJ190384.1|BJ190384
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGGGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|18372637|gb|BJ204239.1|BJ204239
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|100373109|gb|BY949215.1|BY949215
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|162157447|gb|FC333211.1|FC333211
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|100383769|gb|BY969298.1|BY969298
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|100361559|gb|BY984067.1|BY984067
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|18327150|gb|BJ159151.1|BJ159151
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|208364270|gb|DC935541.1|DC935541
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|18362471|gb|BJ194541.1|BJ194541
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGGGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|100358066|gb|BY965455.1|BY965455
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
EST: gi|18329338|gb|BJ161344.1|BJ161344
EST:     CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAG                         GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG
genomic: CTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG

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: 35 (upstream exon), 35 (downstream exon)
Score: 22

GGCTTTCAAGAAGGACAACAGCGAGAAGAAGCTGAACTTGGGAGTAGGTGCTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaata ... atctttacagGCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTTTCAAGAAGGACAACAGCGAGAAGAAGCTGAACTTGGGAGTAGGTGCTTACCGAACTGAGGATCTCCAGCCCTATGTATTGGAGGTCGTTAAGAAGgtaaacaatatctgcttggcaatgtaccacataccatccttcagaaagtgccactgattcaagtcgtctcaaatacagcttctcctattgtgccacttttgctctctgagcgaagcattaaccatcaggctcaggagtgtttagaaggtatctgattctttcaatctttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG