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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagttgtgcattttgctctagctcatttaatttatatcagttggaacttcattcagttcattcgcttataatatatgtgaaattttggtgttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAAAATGAGCAGCTAGCTTTCTGCCCTGGTGTTATTGTTCCTGGAATCTATT

Basic information

species Physcomitrella patens
transcript PP1S3_353V6.2
intron # 6
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|19790424|gb|BQ041863.1|BQ041863
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTC
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTC
EST: gi|162160440|gb|FC337441.1|FC337441
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|208349639|gb|DC922029.1|DC922029
EST:     CCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTTCGCTGA
genomic: CCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTC-TTCGCTGA
EST: gi|208400784|gb|DC925064.1|DC925064
EST:     GATGATACTAAGA-TTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTTTTCGCTGAA
genomic: GATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162242107|gb|FC414475.1|FC414475
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|208375064|gb|DC956432.1|DC956432
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCCTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162212518|gb|FC388494.1|FC388494
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|208384341|gb|DC928092.1|DC928092
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162174027|gb|FC350542.1|FC350542
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|208366354|gb|DC947564.1|DC947564
EST:     TGGATGATANTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: TGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162160439|gb|FC337440.1|FC337440
EST:     TGAGGACATGTTTCCCTTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: TGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|208352003|gb|DC925812.1|DC925812
EST:     TGAGGACATGNTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: TGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162196447|gb|FC373047.1|FC373047
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|208398319|gb|DC920718.1|DC920718
EST:     ATCCT-NGGATGATACTAAGA-TTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTTCGCTGA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTC-TTCGCTGA
EST: gi|162277339|gb|FC453145.1|FC453145
EST:     AGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: AGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162196446|gb|FC373046.1|FC373046
EST:     GATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: GATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162198044|gb|FC372071.1|FC372071
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATAACGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|208356230|gb|DC918428.1|DC918428
EST:     TGGATGATACTAAGATTTGNCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGA
genomic: TGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGT-GGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGA
EST: gi|37853129|gb|BJ611137.1|BJ611137
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCNTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162277340|gb|FC453146.1|FC453146
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|208352941|gb|DC921811.1|DC921811
EST:     GCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAA-TTNTTCGCTGAA
genomic: GCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162242106|gb|FC414474.1|FC414474
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162152467|gb|FC328030.1|FC328030
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|162225093|gb|FC401717.1|FC401717
EST:     ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
EST: gi|208352552|gb|DC918261.1|DC918261
EST:     ATCCTCTGGATGATACTAAGA-TTGGCCTGAGGACATGTTT-CCCTTCAG                         CCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA
genomic: ATCCTCTGGATGATACTAAGATTTGGCCTGAGGACATGTTTCCCCTTCAGgtatgtctcc ... ttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcattcagttcattcgcttataatatatgtgaaattttggtgttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAAAATGAGCAGCTAGCTTTCTGCCCTGGTGTTATTGTTCCTGGAATCTATT
                    ttataatatatgtgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagttgtgcattttgctctagctcatttaatttatatcagttggaacttcattcagttcattcgcttataatatatgtgaaattttggtgttgcacgcagCCTGTGGGAAGGATGGTGCTGAACAGGAATATCGACAATTTCTTCGCTGAAAATGAGCAGCTAGCTTTCTGCCCTGGTGTTATTGTTCCTGGAATCTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT