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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAAAACTCCCTCAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagttttgctgttctgccatttgcattctcgtatctgcattatagtccaaggatgtggatgttcggatgctgaactggtcgttttctaagagattgtctgtccttccag

Basic information

species Physcomitrella patens
transcript PP1S209_135V6.1
intron # 2
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|18350329|gb|BJ182380.1|BJ182380
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|18351887|gb|BJ183939.1|BJ183939
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|18373193|gb|BJ204795.1|BJ204795
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|18325961|gb|BJ157960.1|BJ157960
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|100360816|gb|BY965915.1|BY965915
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|162194102|gb|FC370277.1|FC370277
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|18360367|gb|BJ192429.1|BJ192429
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|18369571|gb|BJ201659.1|BJ201659
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|18363051|gb|BJ195123.1|BJ195123
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|18348401|gb|BJ180449.1|BJ180449
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|208368222|gb|DC931448.1|DC931448
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|67508066|gb|BJ940937.1|BJ940937
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|208353659|gb|DC929702.1|DC929702
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|18361973|gb|BJ194040.1|BJ194040
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
EST: gi|18329732|gb|BJ161738.1|BJ161738
EST:     CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTG                         AGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG
genomic: CAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAG

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: 34 (upstream exon), 25 (downstream exon)
Score: 7

AAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAAAACTCCCTCAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagtttt ... gtccttccagAGGTGGAGGGCTTGAAGCTTCGACATTTCGTTGATGAACCCACTTATACAGACCTTCACTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAGGACAGGGTGAGGCTAGCCCGCAAGGACCTCTACAAAAACTCCCTCAGGAAGGCTGGTCATGCATGGAAGACTATCTTGGAAAAGGGATTATCTGgtacagttttgctgttctgccatttgcattctcgtatctgcattatagtccaaggatgtggatgttcggatgctgaactggtcgttttctaagagattgtctgtccttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA