Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcttcgatcaacaaagaagcacatgcagtgttagagagcttgcacatgtttctttactccatcttgcattatcttttgtattttttctctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTGTTGCGTGATGTTGCAAAG

Basic information

species Physcomitrella patens
transcript PP1S84_144V6.2
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|100353027|gb|BY945570.1|BY945570
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100398455|gb|BY972613.1|BY972613
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|208353098|gb|DC910149.1|DC910149
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100425397|gb|BY958574.1|BY958574
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100387101|gb|BY951500.1|BY951500
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100446389|gb|CJ970688.1|CJ970688
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100370255|gb|BY985320.1|BY985320
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100409896|gb|BY974309.1|BY974309
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100385037|gb|BY987500.1|BY987500
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100385459|gb|BY969796.1|BY969796
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100425973|gb|BY977213.1|BY977213
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100433241|gb|BY960528.1|BY960528
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100419885|gb|BY975897.1|BY975897
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100447372|gb|CJ971671.1|CJ971671
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
EST: gi|100359446|gb|BY984258.1|BY984258
EST:     GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAG                         GTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG
genomic: GTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTG

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), 31 (downstream exon)
Score: 14

AAAGGAGCACGTCATTCATGGGTTGCAGGAGCGTATTTCGAAGGCCACAGGTGCCTTGCAAGAACAAAGTGCCAAGCTTTCGCATTCTGAAGCCGAACAGgtctttctat ... ctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTGTTGCGTGATGTTGCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtttctttactccatcttgcattatcttttgtattttttctctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTGTTGCGTGATGTTGCAAAG
                       cattatcttttgtatt  CT-rich tract
                        attatcttttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcttcgatcaacaaagaagcacatgcagtgttagagagcttgcacatgtttctttactccatcttgcattatcttttgtattttttctctctttgcagGTGAAGCTGGTCAATGAAAAGAACGCACTTGCAACTCAAGTGAAAAATTTGTTGCGTGATGTTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - -cacatgc
- - - - - - - - - - - - - - - - - - - - -ttgcaca