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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaagatacagtttcattcgtacttgaacacgaagtcctcaagggatcaaccatgagtcctaatgtccaatcctgcacttattttgatgtttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGACAGGAACAGGAGTTATTGCTGGAGGTGCTGTGCGTGTGGTGCTTGAGTTG

Basic information

species Physcomitrella patens
transcript PP1S61_236V6.1
intron # 2
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|67727450|gb|BJ977709.1|BJ977709
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162236121|gb|FC411942.1|FC411942
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|208385976|gb|DC956492.1|DC956492
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162170725|gb|FC346312.1|FC346312
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGC
EST: gi|19787005|gb|BQ040567.1|BQ040567
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162208995|gb|FC385547.1|FC385547
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|18340868|gb|BJ172899.1|BJ172899
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162236107|gb|FC411941.1|FC411941
EST:     TTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: TTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|208352574|gb|DC918283.1|DC918283
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162264700|gb|FC441698.1|FC441698
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162188538|gb|FC363720.1|FC363720
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCANGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162244028|gb|FC422344.1|FC422344
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|67696735|gb|BJ956968.1|BJ956968
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|208381259|gb|DC919149.1|DC919149
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162252428|gb|FC427822.1|FC427822
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGGGGGGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|208350113|gb|DC921480.1|DC921480
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162264699|gb|FC441697.1|FC441697
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|18338414|gb|BJ170438.1|BJ170438
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|208381849|gb|DC923401.1|DC923401
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|208347468|gb|DC925380.1|DC925380
EST:     TGTGCCCATGACCNAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: TGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162159309|gb|FC335136.1|FC335136
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
EST: gi|162190806|gb|FC367068.1|FC367068
EST:     CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAG                         AGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC
genomic: CGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGAC

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: 31 (upstream exon), 34 (downstream exon)
Score: 27

CTGCGAAGGAGGTCATTACTGCCGTGCAGAAGTCGGCTACTGACGCCCGGCGCCACTTGGTCACTGTGCCCATGACCAAGTACCTGACATTCCCACACAGgtacatactc ... tttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGACAGGAACAGGAGTTATTGCTGGAGGTGCTGTGCGTGTGGTGCTTGAGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcaaccatgagtcctaatgtccaatcctgcacttattttgatgtttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGACAGGAACAGGAGTTATTGCTGGAGGTGCTGTGCGTGTGGTGCTTGAGTTG
                                             tttatctc  CT-rich tract
                                  ttattttgatgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaagatacagtttcattcgtacttgaacacgaagtcctcaagggatcaaccatgagtcctaatgtccaatcctgcacttattttgatgtttatctcagAGCCGATGGAGAATACGGTGCAGCCAAGGTGATGCTCAGGCCTGCGGCGACAGGAACAGGAGTTATTGCTGGAGGTGCTGTGCGTGTGGTGCTTGAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctgca