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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatcttctgaagagaccttagagagttctttaggtttttgttagaaaattaattaatttattaattaatttcctccacttacaagctgtgcttg...

Basic information

species Physcomitrella patens
transcript PP1S207_28V6.1
intron # 5
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|162272681|gb|FC448307.1|FC448307
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|208383342|gb|DC907517.1|DC907517
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|67573864|gb|BJ946688.1|BJ946688
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|208370398|gb|DC931810.1|DC931810
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAA
EST: gi|208394358|gb|DC904178.1|DC904178
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|100395348|gb|BY953692.1|BY953692
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|162263698|gb|FC439623.1|FC439623
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|162202372|gb|FC379991.1|FC379991
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|100387386|gb|BY988257.1|BY988257
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGCTGAAACAAGAAAAGGATGTCAGACT
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACT
EST: gi|208399872|gb|DC904954.1|DC904954
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|162264593|gb|FC440889.1|FC440889
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|208397168|gb|DC911777.1|DC911777
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|162217121|gb|FC392485.1|FC392485
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|208391589|gb|DC933838.1|DC933838
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATACTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTGGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|162278437|gb|FC454523.1|FC454523
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|208393061|gb|DC929556.1|DC929556
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGCAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|162175835|gb|FC352137.1|FC352137
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
EST: gi|208359117|gb|DC930449.1|DC930449
EST:     AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAG                         GTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA
genomic: AGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAA

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: 22 (upstream exon), 15 (downstream exon)
Score: 2

GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatc ... gtaagaacagGTCTACGACTGGTTGAAACAAGAAAAGGATGTCAGACTTGGTGACTGGAAAACTGCCGAAATTGAGATTCTGAATACATTCCAGTTGCTGTCTGCAAAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACATTGAATTCATGGAGAAGAAAATTGACGACTGTGAAAAAGTCTTGAAGCGCAGCAATGCTAAGGAAGCGAAAATGGAATTGGAATGCTGTCAAAAGgtccgttatcttctgaagagaccttagagagttctttaggtttttgttagaaaattaattaatttattaattaatttcctccacttacaagctgtgcttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG