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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGAAGACGCTCTCAAGGAAGGAATGGGTGGAGGTGGAGGGCACAACCCATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccgatttaagctaaaaatttgtctttctttgttgtggattcgaattcattctcttactgtttttctttctcgctgtggacatgtgagcaattactaagtaactgagatcgatctcctgattgccag

Basic information

species Physcomitrella patens
transcript PP1S174_37V6.1
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|100402414|gb|BY954824.1|BY954824
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|162153711|gb|FC329114.1|FC329114
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|162152004|gb|FC327918.1|FC327918
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|162197042|gb|FC375241.1|FC375241
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|162180092|gb|FC356657.1|FC356657
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|100431293|gb|BY960124.1|BY960124
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|208373708|gb|DC936535.1|DC936535
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|67574368|gb|BJ947192.1|BJ947192
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGA
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGA
EST: gi|208358355|gb|DC934548.1|DC934548
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCG
EST: gi|162213966|gb|FC390165.1|FC390165
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|162151466|gb|FC326971.1|FC326971
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|100407617|gb|BY991778.1|BY991778
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|162173994|gb|FC350509.1|FC350509
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|208353142|gb|DC910151.1|DC910151
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGNA-GTGGGANGGGTGGTA
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTA
EST: gi|208359865|gb|DC934866.1|DC934866
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGANGGGTGGTAGCAGGCGACAAAGGAGA
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGA
EST: gi|100441954|gb|BY981177.1|BY981177
EST:     TTTGACATCTTCGAGTCATTCTTTGGCGGGGGTGGGAAGCCCATTTGGAG                         ATTCATTTCCGGGCGGAAGTGGGAAGGGGTGGTAGCAGGCGACAAAGGAGA
genomic: TTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGG-AAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGA-GGGGTGGTAGCAGGCGACAAAGGAGA
EST: gi|162263312|gb|FC439094.1|FC439094
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|162166513|gb|FC343210.1|FC343210
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|100392962|gb|BY989694.1|BY989694
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         AT-CATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCA
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCA
EST: gi|100384322|gb|BY969453.1|BY969453
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
EST: gi|67569005|gb|BJ941829.1|BJ941829
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAAGTGGGAGGGGTGGTAGCAGGCGA
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAA-GTGGGAGGGGTGGTAGCAGGCGA
EST: gi|100396849|gb|BY953858.1|BY953858
EST:     ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAG                         ATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG
genomic: ATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAG

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: 186

GGAGAAGACGCTCTCAAGGAAGGAATGGGTGGAGGTGGAGGGCACAACCCATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccga ... tgattgccagATTCATTTCCTGGCGGAAGTGGGAGGGGTGGTAGCAGGCGACAAAGGAGAGGGGAAGATGTAGTTCATCCTTTGAAGGTTTCATTGGAAGATCTTTACAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGAAGACGCTCTCAAGGAAGGAATGGGTGGAGGTGGAGGGCACAACCCATTTGACATCTTCGAGTCATTCTTTGGCGGTGGTGGAAGCCCATTTGGAGgtacacccgatttaagctaaaaatttgtctttctttgttgtggattcgaattcattctcttactgtttttctttctcgctgtggacatgtgagcaattactaagtaactgagatcgatctcctgattgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG