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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGAGGCAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgccacattgctgcagcatttgcaggaaaggacattcaaatctttcatggaaactccatgcactatgttgacttccttgaaagacactgtgttg...

Basic information

species Physcomitrella patens
transcript PP1S205_25V6.1
intron # 8
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|162280482|gb|FC456395.1|FC456395
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|208371212|gb|DC956004.1|DC956004
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|67724192|gb|BJ974451.1|BJ974451
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162170103|gb|FC347015.1|FC347015
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162177265|gb|FC353422.1|FC353422
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162179280|gb|FC356229.1|FC356229
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|208359054|gb|DC957802.1|DC957802
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|208354342|gb|DC953790.1|DC953790
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162179279|gb|FC356228.1|FC356228
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162227183|gb|FC402826.1|FC402826
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|37832669|gb|BJ590681.1|BJ590681
EST:     CAACCATGCCAGAAGAGGAGGCTCGTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162159392|gb|FC334660.1|FC334660
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|208357076|gb|DC926507.1|DC926507
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162177061|gb|FC353114.1|FC353114
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162178856|gb|FC354788.1|FC354788
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162167604|gb|FC344256.1|FC344256
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|208347204|gb|DC949745.1|DC949745
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|37840478|gb|BJ598486.1|BJ598486
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162203866|gb|FC379963.1|FC379963
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162181031|gb|FC358685.1|FC358685
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162167605|gb|FC344257.1|FC344257
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162278585|gb|FC454047.1|FC454047
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162280481|gb|FC456394.1|FC456394
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162203867|gb|FC379964.1|FC379964
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|208361679|gb|DC954127.1|DC954127
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162153878|gb|FC330009.1|FC330009
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162179456|gb|FC355456.1|FC355456
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162187678|gb|FC364629.1|FC364629
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162177062|gb|FC353115.1|FC353115
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGT
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGT
EST: gi|208381579|gb|DC915445.1|DC915445
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|37836121|gb|BJ594129.1|BJ594129
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|208360740|gb|DC946464.1|DC946464
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162169104|gb|FC345994.1|FC345994
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATTTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|37844248|gb|BJ602256.1|BJ602256
EST:     GTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: GTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162177266|gb|FC353423.1|FC353423
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162170104|gb|FC347016.1|FC347016
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|67698740|gb|BJ958973.1|BJ958973
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
EST: gi|162227182|gb|FC402825.1|FC402825
EST:     CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAG                         ACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA
genomic: CAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACA

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), 31 (downstream exon)
Score: 12

TCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGAGGCAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgcc ... tcgtgaacagACACACATGAGCGAAATGTTCGCGTTTCATGCCACCTTGATGTCGAACACATTAGGGACGTCAATATGCGTGTTCACACGTTCAGGTTTCATGGCGCTCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCATTGAAAGCCGTGCGAGTGATGCATACTGTGGCTATGCGCACGGAGGCAACCATGCCAGAAGAGGAGGCTCCTTCAAATCTTGGTCGAGCATTTAAGgtactacgccacattgctgcagcatttgcaggaaaggacattcaaatctttcatggaaactccatgcactatgttgacttccttgaaagacactgtgttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG