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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcattaactatgaggatttcgttgcgaccatcactgattgattactactacatataattctgttgtgaagtggtttgggtgctgcttttactgttgagattaaatttattgtctgaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAGGATATTCCCATGGCCAACCTTGTAGAGAAGATCGGCGAGATCTTGGAAA

Basic information

species Physcomitrella patens
transcript PP1S7_175V6.1
intron # 8
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|18339632|gb|BJ171659.1|BJ171659
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162238449|gb|FC414587.1|FC414587
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|37829899|gb|BJ587911.1|BJ587911
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162173416|gb|FC349795.1|FC349795
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162224268|gb|FC399514.1|FC399514
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|37841561|gb|BJ599569.1|BJ599569
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|67699791|gb|BJ960024.1|BJ960024
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|37828261|gb|BJ586273.1|BJ586273
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162264776|gb|FC440343.1|FC440343
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162215796|gb|FC390861.1|FC390861
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|208351458|gb|DC926304.1|DC926304
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCNGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162250112|gb|FC427421.1|FC427421
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162258850|gb|FC434857.1|FC434857
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162237814|gb|FC413923.1|FC413923
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|37827562|gb|BJ585574.1|BJ585574
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162158159|gb|FC333954.1|FC333954
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162173417|gb|FC349796.1|FC349796
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAANACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|37825576|gb|BJ583642.1|BJ583642
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|37826374|gb|BJ584386.1|BJ584386
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|37853519|gb|BJ611527.1|BJ611527
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|19779686|gb|BQ039466.1|BQ039466
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162224254|gb|FC399513.1|FC399513
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162264775|gb|FC440342.1|FC440342
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162215795|gb|FC390860.1|FC390860
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
EST: gi|162258851|gb|FC434858.1|FC434858
EST:     GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAG                         GTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG
genomic: GTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAG

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), 22 (downstream exon)
Score: 13

GAGAGATAATTACTCTCCTGGATGGAAGTACTCTCATTGGGAGCTAAAAGGTGTACCCTTGAGAATTGAAATTGGTCCCAGGGACATTGAAAATAAGCAGgtatagcatt ... gaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAGGATATTCCCATGGCCAACCTTGTAGAGAAGATCGGCGAGATCTTGGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtttgggtgctgcttttactgttgagattaaatttattgtctgaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAGGATATTCCCATGGCCAACCTTGTAGAGAAGATCGGCGAGATCTTGGAAA
                             attaaatttattgtct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagcattaactatgaggatttcgttgcgaccatcactgattgattactactacatataattctgttgtgaagtggtttgggtgctgcttttactgttgagattaaatttattgtctgaaattacagGTTCGAGTCGTTCGTCGAGACTTGGAAGATAAAACTGAGGGGCGATCTCAGGATATTCCCATGGCCAACCTTGTAGAGAAGATCGGCGAGATCTTGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC