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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggattaactctgaaatggtgttcctaccatatttattgaaattctggtaggcaacggttttggggtctcaagggaaggtcatacgtgcttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGCGGCCATTCACTGGGGGCGCCATAGATTTCAGGCGTGCTACAGCTCCTCT

Basic information

species Physcomitrella patens
transcript PP1S205_59V6.2
intron # 2
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|100391111|gb|BY953121.1|BY953121
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|208345596|gb|DC909280.1|DC909280
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|18368524|gb|BJ200609.1|BJ200609
EST:     GTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: GTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAA-GTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|100352848|gb|BY945480.1|BY945480
EST:     CGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|100387062|gb|BY951461.1|BY951461
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|100401955|gb|BY973143.1|BY973143
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|100380439|gb|BY986696.1|BY986696
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|162165615|gb|FC341454.1|FC341454
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAACAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|208400638|gb|DC904838.1|DC904838
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|162168296|gb|FC344610.1|FC344610
EST:     GGGCAGCCGCGGATGGCAACAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: GGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|100389334|gb|BY971084.1|BY971084
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|100436235|gb|BY979447.1|BY979447
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|100446273|gb|CJ970572.1|CJ970572
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|100433189|gb|BY978850.1|BY978850
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|67569854|gb|BJ942678.1|BJ942678
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|100437353|gb|BY961478.1|BY961478
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|100447186|gb|CJ971485.1|CJ971485
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
EST: gi|162258767|gb|FC434566.1|FC434566
EST:     TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTG                         GGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC
genomic: TGTTACAGGCGTTAGGGCAGCCGCGGATGGCAGCAGGGAAGTTGGTTTTGgtaagctctt ... ttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtaggcaacggttttggggtctcaagggaaggtcatacgtgcttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGCGGCCATTCACTGGGGGCGCCATAGATTTCAGGCGTGCTACAGCTCCTCT
                                           gcttgat  putative branch site (score: 5)
                                             ttgatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggattaactctgaaatggtgttcctaccatatttattgaaattctggtaggcaacggttttggggtctcaagggaaggtcatacgtgcttgattttagGGACAACGAAAGGCGTAGCACTGAATGGGAATGGAACAATGGTGACCGAGCGGCCATTCACTGGGGGCGCCATAGATTTCAGGCGTGCTACAGCTCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC