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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggagtggatgtctttgagaatctctagtattttaggtgaatgataagataagtttttgacacgacctaataatccgggggggggggggttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCATGCTACCTTTGTGCCCCATACCGCTGGACGGTACTCCGTGAAGCGTTTTA

Basic information

species Physcomitrella patens
transcript PP1S101_208V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_208V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT3G11940.2 (Arabidopsis thaliana), 3'ss of exon 2
----ttggagtggatgtctttgagaatctctagtattttaggtgaatgataagataagtttttgacacgacctaataatccgggggggggggggttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCATGCTACCTTTGTGCCCCATACCGCTGGACGGTACTCCGTGAAGCGTTTTA
    ||    | | |  ||    || |   |     ||| || |  |  || |  |  || ||         || | |     |          |  |||  || |||  ||||||    | |  ||||||||||  ||    |  |  || |||||||||||||| ||||| ||||||||| | ||||| |||||| | || |
gtttttcattttgctccctgaatgattggatctccgttttggcgt-tagtatgtcagattcttagtgttgt-tagtgacaattgttttttttcatcttgt--agGTCACAGACATCAGTCTTGTTGACTACATTGGAGTTCAGGCAGCTAAACATGCTACCTTTGTTCCCCACACCGCTGGAAGATACTCTGTGAAGAGATTCA
















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|37850596|gb|BJ608604.1|BJ608604
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|37839850|gb|BJ597858.1|BJ597858
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCAGTGGACAAGCA
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagAT-CAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCA
EST: gi|67720078|gb|BJ970337.1|BJ970337
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|67701589|gb|BJ961822.1|BJ961822
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|18362582|gb|BJ194653.1|BJ194653
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCAGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|18338455|gb|BJ170479.1|BJ170479
EST:     GTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: GTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|37839339|gb|BJ597347.1|BJ597347
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCAGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|67696498|gb|BJ956731.1|BJ956731
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|67725656|gb|BJ975915.1|BJ975915
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|162243879|gb|FC423196.1|FC423196
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|162243102|gb|FC416702.1|FC416702
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|67697648|gb|BJ957881.1|BJ957881
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|162241814|gb|FC418069.1|FC418069
EST:     GAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: GAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|162241659|gb|FC415535.1|FC415535
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|18361640|gb|BJ193706.1|BJ193706
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCAGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|67572736|gb|BJ945560.1|BJ945560
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|67726461|gb|BJ976720.1|BJ976720
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCACTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|67717134|gb|BJ967393.1|BJ967393
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|67574244|gb|BJ947068.1|BJ947068
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|18369285|gb|BJ201370.1|BJ201370
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|162243878|gb|FC423195.1|FC423195
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCGGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|67573113|gb|BJ945937.1|BJ945937
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|18368029|gb|BJ200113.1|BJ200113
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|162243101|gb|FC416701.1|FC416701
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|67717958|gb|BJ968217.1|BJ968217
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCACTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
EST: gi|162266196|gb|FC441725.1|FC441725
EST:     CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAG                         ATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT
genomic: CGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCAT

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), 33 (downstream exon)
Score: 26

CCCAGCAGTCGACGACGACACCCCCTTCCGTGTTGCAGTCATGGCGGTTGCGCAGCCAGAAGTGAAGCTATTCGGGCGCTGGTCATTCGATGACATCGAGgtttgtgttt ... ttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCATGCTACCTTTGTGCCCCATACCGCTGGACGGTACTCCGTGAAGCGTTTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagataagtttttgacacgacctaataatccgggggggggggggttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCATGCTACCTTTGTGCCCCATACCGCTGGACGGTACTCCGTGAAGCGTTTTA
                    acctaat  putative branch site (score: 26)
     taagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggagtggatgtctttgagaatctctagtattttaggtgaatgataagataagtttttgacacgacctaataatccgggggggggggggttgtgtccagATCAATGACATCTCCTTGGCCGACTACATTGCCGTGTCCGTGGACAAGCATGCTACCTTTGTGCCCCATACCGCTGGACGGTACTCCGTGAAGCGTTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC