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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTGAGGAATCCGCATTCGTGGCCCCCGGTGCTTCTGTTGTTGGTGAAGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagttaattcgtccatcctccgtgtgtttctcaagctatgaggcagtatcacaaggctgaatcattttcaaacatcgtagttatcttagtgtcag...

Basic information

species Physcomitrella patens
transcript PP1S207_12V6.1
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|162233651|gb|FC409410.1|FC409410
EST:     AGTGGAAATTGGAAAGCAGTCGTCAGTNTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
EST: gi|18369330|gb|BJ201416.1|BJ201416
EST:     AGTGGAAATTGGAAGGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
EST: gi|18363020|gb|BJ195092.1|BJ195092
EST:     AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
EST: gi|208349491|gb|DC905629.1|DC905629
EST:     AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
EST: gi|67697542|gb|BJ957775.1|BJ957775
EST:     AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
EST: gi|37834717|gb|BJ592729.1|BJ592729
EST:     AAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGGACAAT
genomic: AAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCA-GGACAAT
EST: gi|18353257|gb|BJ185312.1|BJ185312
EST:     AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATC
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATC
EST: gi|37840237|gb|BJ598245.1|BJ598245
EST:     AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
EST: gi|18350228|gb|BJ182279.1|BJ182279
EST:     AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
EST: gi|208381510|gb|DC919512.1|DC919512
EST:     AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
EST: gi|37850643|gb|BJ608651.1|BJ608651
EST:     AGTGGAAATTGGAAGGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
EST: gi|67574145|gb|BJ946969.1|BJ946969
EST:     AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
EST: gi|162233652|gb|FC409411.1|FC409411
EST:     AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAG                         GTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA
genomic: AGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATA

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: 34 (upstream exon), 35 (downstream exon)
Score: 4

GTCATTGAGGAATCCGCATTCGTGGCCCCCGGTGCTTCTGTTGTTGGTGAAGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagtt ... tatgtggcagGTGATGTTCATCATATCAAAGTGGGATCAGAGACGAATATTCAGGACAATACTGTAGTACATGTAGCCAAAACCAACGTAAGTGGCAATGTTGAGCCTAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTGAGGAATCCGCATTCGTGGCCCCCGGTGCTTCTGTTGTTGGTGAAGTGGAAATTGGAAAGCAGTCGTCAGTTTGGTACGGATGTGTTCTACGAGgtaagaagttaattcgtccatcctccgtgtgtttctcaagctatgaggcagtatcacaaggctgaatcattttcaaacatcgtagttatcttagtgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA