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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGCTGTATTCAGCTGACGCTGATTTCTCGTGTTTCGCGGATCTAGCATTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatcccggtctttattcccatgcaaattgtgaatcgttagtctttgtttgggttcagtttgtatgtcatgcgcataggagttacgtaataatgggtacatttgtgtatgagcag

Basic information

species Physcomitrella patens
transcript PP1S277_10V6.3
intron # 9
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|162192890|gb|FC369884.1|FC369884
EST:     TGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTNCA                         -GCGGTTTTGACTCCCGGAGATCCATATATGCCCCTGCCAAATGAAAAG
genomic: TGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATT-CAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAG
EST: gi|162230034|gb|FC405974.1|FC405974
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162151766|gb|FC328623.1|FC328623
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162167139|gb|FC343615.1|FC343615
EST:     TTGACTTCACNTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162166538|gb|FC343235.1|FC343235
EST:     GACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: GACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|18333028|gb|BJ165042.1|BJ165042
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162264024|gb|FC439254.1|FC439254
EST:     GACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: GACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|37847706|gb|BJ605714.1|BJ605714
EST:     TTGACTTCACNTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162150291|gb|FC326376.1|FC326376
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162198692|gb|FC373473.1|FC373473
EST:     CTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: CTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162274126|gb|FC450198.1|FC450198
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162174878|gb|FC351670.1|FC351670
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162267925|gb|FC444006.1|FC444006
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|37852887|gb|BJ610895.1|BJ610895
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|208356633|gb|DC922423.1|DC922423
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCCCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|18341056|gb|BJ173089.1|BJ173089
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162225911|gb|FC400955.1|FC400955
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162155412|gb|FC332026.1|FC332026
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|208349557|gb|DC921989.1|DC921989
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162215092|gb|FC391562.1|FC391562
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGATTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162151767|gb|FC328624.1|FC328624
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162150290|gb|FC326375.1|FC326375
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|208383087|gb|DC919534.1|DC919534
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|18335957|gb|BJ167978.1|BJ167978
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162241669|gb|FC418652.1|FC418652
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|37844529|gb|BJ602537.1|BJ602537
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|37850391|gb|BJ608399.1|BJ608399
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|100358217|gb|BY965531.1|BY965531
EST:     TGACTTCACCTGAGGACTACTANCAA-GAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGG
genomic: TGACTTCACCTGAGGACTACTA-CAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGG
EST: gi|162262810|gb|FC439255.1|FC439255
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|18334473|gb|BJ166490.1|BJ166490
EST:     TTGACTTCACNTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|208395110|gb|DC923909.1|DC923909
EST:     TTGACTTCACCCGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162192889|gb|FC369883.1|FC369883
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162241668|gb|FC418651.1|FC418651
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|18337566|gb|BJ169590.1|BJ169590
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162167476|gb|FC344193.1|FC344193
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162170375|gb|FC346780.1|FC346780
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|18335620|gb|BJ167640.1|BJ167640
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162151153|gb|FC327152.1|FC327152
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
EST: gi|162188826|gb|FC364840.1|FC364840
EST:     TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCA                         AGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT
genomic: TTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGT

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: 24 (upstream exon), 28 (downstream exon)
Score: 3

ATCTGCTGTATTCAGCTGACGCTGATTTCTCGTGTTTCGCGGATCTAGCATTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatc ... gtatgagcagAGCGGTTTTGACTCCCGGAGATCCATATATGCCCTTGCCAAATGAAAAGGTGGTGAAGGCCGTCCATGAACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGCTGTATTCAGCTGACGCTGATTTCTCGTGTTTCGCGGATCTAGCATTGACTTCACCTGAGGACTACTACAAAGAAGGAGAAGGCTCTCTTATTCAgtaagttatcccggtctttattcccatgcaaattgtgaatcgttagtctttgtttgggttcagtttgtatgtcatgcgcataggagttacgtaataatgggtacatttgtgtatgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA