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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTTCTCTTTCGGATTTGTTGTTGCCCGGAGTGTGTGTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgctctaaagcgagctctctgtgcactgtcccaccctcctttccatttcccttcgctcccccacgttccttctctctcttgtagtgccttttc...

Basic information

species Physcomitrella patens
transcript PP1S282_25V6.1
intron # 1
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|67710125|gb|BJ965862.1|BJ965862
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|162179274|gb|FC356223.1|FC356223
EST:     CCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: CCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|18367098|gb|BJ199178.1|BJ199178
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|18360158|gb|BJ192220.1|BJ192220
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|162190843|gb|FC368041.1|FC368041
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|18368232|gb|BJ200317.1|BJ200317
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|208372562|gb|DC940809.1|DC940809
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|162258719|gb|FC434518.1|FC434518
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|18371206|gb|BJ202808.1|BJ202808
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|162280391|gb|FC456096.1|FC456096
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|18325295|gb|BJ157291.1|BJ157291
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|162170018|gb|FC345071.1|FC345071
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|162206405|gb|FC383398.1|FC383398
EST:     GCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|18366461|gb|BJ198540.1|BJ198540
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|67572957|gb|BJ945781.1|BJ945781
EST:     TGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: TGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|67718208|gb|BJ968467.1|BJ968467
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|18327820|gb|BJ159824.1|BJ159824
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|18325583|gb|BJ157580.1|BJ157580
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|18366927|gb|BJ199007.1|BJ199007
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
EST: gi|208346219|gb|DC909525.1|DC909525
EST:     GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATG                         GCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG
genomic: GTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGG

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: 23 (upstream exon), 34 (downstream exon)
Score: 22

GGTTTCTCTTTCGGATTTGTTGTTGCCCGGAGTGTGTGTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgc ... ttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGGATGCTTGACAAGCTGGGTGGCGCCTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTTCTCTTTCGGATTTGTTGTTGCCCGGAGTGTGTGTCCTGCCGCCTCGCACCCTCGCAGCGCCAGCTCCTGCCTTCCCACCATGgtatctacgctctaaagcgagctctctgtgcactgtcccaccctcctttccatttcccttcgctcccccacgttccttctctctcttgtagtgccttttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC