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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCGACACTAGGGTCCATGCTGCTAATAAGCTAGCCAATAAGCATGTCCGCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacattacggttttcgtatttcaccaaaaaaaaattaaaattaaattaaaaataagatcgacattgtgagcacacgtactaggttccattaccgc...

Basic information

species Physcomitrella patens
transcript PP1S98_84V6.2
intron # 2
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|162245599|gb|FC424127.1|FC424127
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|162229735|gb|FC404019.1|FC404019
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|208368426|gb|DC935991.1|DC935991
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|18330765|gb|BJ162771.1|BJ162771
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGA
EST: gi|18330923|gb|BJ162929.1|BJ162929
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|100372576|gb|BY985666.1|BY985666
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|100416857|gb|BY993124.1|BY993124
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|208378757|gb|DC914731.1|DC914731
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|100452996|gb|CJ975548.1|CJ975548
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|208385375|gb|DC956615.1|DC956615
EST:     CGTGCCTCTTGTTNGACAGCTTGAGCCTTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: CGTGCCTCTTGTTGGACAGCTTGAGCC-TCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|100418392|gb|BY957396.1|BY957396
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|100398110|gb|BY954093.1|BY954093
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|18328498|gb|BJ160503.1|BJ160503
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|208377991|gb|DC914368.1|DC914368
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|162225034|gb|FC401450.1|FC401450
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|208384366|gb|DC928117.1|DC928117
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCNTCCCCGNTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|162233741|gb|FC410007.1|FC410007
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|100442029|gb|BY962922.1|BY962922
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|100443881|gb|BY982109.1|BY982109
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|18348368|gb|BJ180416.1|BJ180416
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|208400107|gb|DC904755.1|DC904755
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|7148073|gb|AW509995.1|AW509995
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTGCCCGCTGCGACATATGTCAG                         GAAAAACCANGTTTGTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
EST: gi|208353978|gb|DC930118.1|DC930118
EST:     GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAG                         GAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA
genomic: GCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGA

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), 35 (downstream exon)
Score: 39

TTGCGACACTAGGGTCCATGCTGCTAATAAGCTAGCCAATAAGCATGTCCGCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacat ... tgtttttcagGAAAAACCAGGTTTCTTTTTCTGCTTGGAAGACAGGGCTCTTCTCTGTCGAGATTGTGATGTGTCCATTCACAGCGCCAACAAGCTGTCCTCCAACCACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCGACACTAGGGTCCATGCTGCTAATAAGCTAGCCAATAAGCATGTCCGCGTGCCTCTTGTTGGACAGCTTGAGCCTCCCCGCTGCGACATATGTCAGgtccgtacattacggttttcgtatttcaccaaaaaaaaattaaaattaaattaaaaataagatcgacattgtgagcacacgtactaggttccattaccgc

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaataa