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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcgtgctggatggggttattggatacgactagtgcttgtagggtttgctttgtttttagccgttactcagtttgtgtgatgtcgttggttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTGCAGCGTAGGTGTCGTAAGCGGAGGCAACCATGGCGAAAAACTCGTTCAA

Basic information

species Physcomitrella patens
transcript PP1S249_49V6.1
intron # 1
splice site 3'
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|162238575|gb|FC418964.1|FC418964
EST:     CTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTGAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|18365712|gb|BJ197789.1|BJ197789
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|37826926|gb|BJ584938.1|BJ584938
EST:     AGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: AGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|22491699|gb|BU051622.1|BU051622
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|18353808|gb|BJ185863.1|BJ185863
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|18325320|gb|BJ157316.1|BJ157316
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|162243663|gb|FC420679.1|FC420679
EST:     CACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTGAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|37835281|gb|BJ593293.1|BJ593293
EST:     TTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: TTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|162260417|gb|FC435043.1|FC435043
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|37845489|gb|BJ603497.1|BJ603497
EST:     GGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: GGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|67570411|gb|BJ943235.1|BJ943235
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|67693686|gb|BJ953919.1|BJ953919
EST:     CGTCTCTTCACCC-TTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|162226589|gb|FC402491.1|FC402491
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTGAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|162244437|gb|FC422610.1|FC422610
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTGAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|162260403|gb|FC435042.1|FC435042
EST:     TCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: TCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|67570144|gb|BJ942968.1|BJ942968
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|162238574|gb|FC418963.1|FC418963
EST:     GAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTGAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: GAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|208375486|gb|DC937001.1|DC937001
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|208392197|gb|DC957276.1|DC957276
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|162237157|gb|FC413524.1|FC413524
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTGAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|162244436|gb|FC422609.1|FC422609
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTGAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|18347837|gb|BJ179884.1|BJ179884
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
EST: gi|162263757|gb|FC438922.1|FC438922
EST:     CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACG                         GTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG
genomic: CGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTG

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), 33 (downstream exon)
Score: 11

TTCGACTCTGCTTCTGCGGTACTGTTCATTCCCTCGCTCTCTCGGCGTTCCGTCTCTTCACCCTTTTCTCTTGAGCAACCACCGGAGTGCGCTACTTACGgtgcgtcgac ... ttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTGCAGCGTAGGTGTCGTAAGCGGAGGCAACCATGGCGAAAAACTCGTTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctttgtttttagccgttactcagtttgtgtgatgtcgttggttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTGCAGCGTAGGTGTCGTAAGCGGAGGCAACCATGGCGAAAAACTCGTTCAA
                                             ttttgtcc  CT-rich tract
     tttgttttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcgtgctggatggggttattggatacgactagtgcttgtagggtttgctttgtttttagccgttactcagtttgtgtgatgtcgttggttttgtccagGTTGATACGGCATCGGTTTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTGCAGCGTAGGTGTCGTAAGCGGAGGCAACCATGGCGAAAAACTCGTTCAA

- - -tgctgga