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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttttttcccaaaagtagatcctgggaagctaatggttgggcattttgtaggactgagcgtttcacccgaataattgatctgtatacttcttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCC

Basic information

species Physcomitrella patens
transcript PP1S37_33V6.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_33V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------ggttttttcccaaaagtagatc------ctggga-agctaatggttgggcattttgtaggactgagcgtttcac-----ccgaataatt------gatctgtatacttcttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCC
                                                             | || |  |  | ||  |        || || |     || |   |||| |  ||    | |  | ||        | | |||  |      |||| | ||  |   | ||  |||| |||||||| || |||||||||||||||||||| ||||||||||||||||  ||| |  ||||||| || ||  | || || |   |  ||||||| |
gtatataaattaactcagtcttcacttttcagatatttgtgaactatcaaagtgaattaactcttgcttatgactatttttattaattgagagaatctctgatgtagcatctgttaatgtttactgattagttattactggatagatctctgagatcagcatgttatgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTACTGGTGGGGAGCCTTTACCTGAGGCTGTACTGTGGCTTC

upper sequence: PP1S37_33V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------ggttttttcccaaaagtagatcctgggaagctaatgg----ttgggcattttgtaggactgagcgtttcacccgaataatt------gatctgtatacttcttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCC
                                                            | || |  |  | ||  |  ||   |  | || |    |  |   |    |  |  ||    | |   | ||||   |      |||| | ||  | | | ||  |||| |||||||| || |||||||||||||||||||| ||||||||||||||||  ||| | |||||||| || ||  | || || |   |  ||||||| |
gtatataaattaactcagtcttcacttttcagatttttgtgactatcaaagtgaattaactcttgcttatgacta--ttttgattaattgatagaatctctgatgtagcttttgtttgttaatatttactgaatggatctctgagatcagcatgttacgtcttatagGGAATTCGCTTTAGGGGCATGTCAATTCCTGAATGCCAGAAAAAGCTTCCAGGTGCTTTTCCTGGTGGGGAGCCTTTGCCTGAGGCTGTACTGTGGCTTC

upper sequence: PP1S37_33V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 5
ggttttttcccaaaagtagatcctgggaagctaatggttgggcattttgtaggactgagcgtttcacccgaataattgatctgtatacttcttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCC
           |    || |   | |    |  || | |     |   ||  ||    |  ||  |     ||||   ||     ||  | ||||  ||||| || || || ||||||||||| |||||||||||||||||||   | ||  |||||    |||| |  || ||  | || ||  |  || ||||||| |
---------gtatggttataattttgatcac--atagataattttcaggtcagatcttgaattagaattatataacatatgatattatcttttgtatcagGGAATACGGTTTAGAGGCATGTCGATTCCTGAATGTCAGAAAATATTACCTTCAGCTGAGTCTGGAGAAGAGCCCTTGCCTGAGAGTCTTCTGTGGCTTC

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|67712952|gb|BJ966401.1|BJ966401
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|162194038|gb|FC370213.1|FC370213
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|162202113|gb|FC378034.1|FC378034
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|18367435|gb|BJ199518.1|BJ199518
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|100452631|gb|CJ975366.1|CJ975366
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATCCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|162165709|gb|FC340890.1|FC340890
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|67574071|gb|BJ946895.1|BJ946895
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|208373915|gb|DC940426.1|DC940426
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|18343965|gb|BJ176004.1|BJ176004
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCCTGAATG
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCC-TGAATG
EST: gi|18346086|gb|BJ178129.1|BJ178129
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|208398177|gb|DC908406.1|DC908406
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|100427449|gb|BY977503.1|BY977503
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|162176173|gb|FC351915.1|FC351915
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|162233299|gb|FC409849.1|FC409849
EST:     GAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|208362586|gb|DC939510.1|DC939510
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|162152562|gb|FC328840.1|FC328840
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|100352729|gb|BY945419.1|BY945419
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|162173170|gb|FC349237.1|FC349237
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|19783472|gb|BQ040017.1|BQ040017
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
EST: gi|162258522|gb|FC434737.1|FC434737
EST:     GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAG                         GGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA
genomic: GCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCA

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), 32 (downstream exon)
Score: 35

GCAATTGGTGGAATGCGCGGCATCAAAGGTATGCTATGGGAGACATCCTTACTTGATCCTGAGGAGgtaagtgcta ... cttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtaggactgagcgtttcacccgaataattgatctgtatacttcttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCC
                            aattgat  putative branch site (score: 35)
                                          cttcttgtt  putative PPT
                         aataattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttttttcccaaaagtagatcctgggaagctaatggttgggcattttgtaggactgagcgtttcacccgaataattgatctgtatacttcttgttgcagGGCATTCGCTTCAGAGGCATGTCAATTCCTGAATGTCAGAAAAAGCTTCCAGCAGCTATACCTGGTGGTGAACCGATCCCCGAAGGCTTTTTGTGGCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG