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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaggtatgatggtgagcggggctcagatggtgttgtaggttgtggtgggatggataattgtggagagctaacgttgagggatggtttgggtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG

Basic information

species Physcomitrella patens
transcript PP1S62_136V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os10g32920.1 (Oryza sativa), 3'ss of exon 2
----ggaggtatgatggtgagcggggctcagatggtgttgtaggttgtgg-tgggatggataattgtggagagctaacgttgagggatggtttgggtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
         |||     ||             |||| || |   |||  | ||  |||     |   | |    || || | | | |   ||||    ||||||||||||||||| ||||| |||||||| ||||| || ||||| |
tttgtacactattcccttggctattttgtcattggttttatcatttggagctgccatgtggtctatcgaattaataccggttatgaa--atttga---tgtgcagACAATGCTGGGGTGATTGTGAATCCCAAGGGTGAGATGAAAG

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G102230_T01 (Zea mays), 3'ss of exon 3
ggaggtatgatggtgagcggggctcagatggtgttgtaggttgtggtgggatggataattgtggagagctaacgttgagggatggtt-tgggtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
     | |  |     || |  |   |          |  |  |   |   ||| |  | ||  |  |||   ||   |   || || || | |  ||||||||||||||| ||||| ||||| || |||||||| ||||| |
ctctttttatttacctgctgctcgtggtcaacaccacatttacttcagccttggttcgtggttcat-gcttctgtaatgttctgtttatgtgatattgcagACAATGCTGGAGTGATTGTGAACCCAAAGGGAGAGATGAAAG

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G078396_T03 (Zea mays), 3'ss of exon 3
ggaggtatgatggtgagcggggctcagatggt----gttgtaggttgtggtgggatggataattgtggagagctaacgttgagggatggtt-tgggtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
     | |  |     || |  ||    ||||     ||  |  |||   |||  |   |    |    | |||   ||   |   || || || | |  ||||||||||||||| ||||| ||||| || |||||||| ||||| |
-----tttatttacctgctgctcttttgtggtctacattagaatttgctttggccttagtttgcggtttgggcttttgtaatgttctgtttatgtggtattgcagACAATGCTGGAGTGATTGTGAACCCAAAGGGAGAGATGAAAG

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G102230_T02 (Zea mays), 3'ss of exon 3
ggaggtatgatggtgagcggggctcagatggtgttgtaggttgtggtgggatggataattgtggagagctaacgttgagggatggtt-tgggtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG----------------------------------------------------------
     | |  |     || |  |   |          |  |  |   |   ||| |  | ||  |  |||   ||   |   || || || | |  ||||||||||||||| ||||| ||||| || |||||||| ||||| |                                                          
ctctttttatttacctgctgctcgtggtcaacaccacatttacttcagccttggttcgtggttcat-gcttctgtaatgttctgtttatgtgatattgcagACAATGCTGGAGTGATTGTGAACCCAAAGGGAGAGATGAAAGGTATACTCCTGAACGTTCTGTTGGTTTTATGTGCATTACAACTATTCTGGTGTAGGCA

upper sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv05s0049g01790.t01 (Vitis vinifera), 3'ss of exon 2
-ggaggtatgatggtgagcggggctcagatggtgttgtaggttgtggtgggatggataattgtggagagctaacgttgag-ggatggtttgggtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
 | |    | ||  |       |    ||   |||  | | |  |  | |  ||| ||||  |  |        | || | | || | |||  ||||  ||||||||||||| || |||||||| || |||||||||||||| |
tgtaatattaatcttcttttttgtattgaaattgtatttgttgttaattgcttggctaatgttctaagatctctgctgtgtgaattggttgaatttg--cagACAATGCTGGTGTCATCGTGAACCCAAAGGGAGAAATGAAAG

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|162224578|gb|FC400474.1|FC400474
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|18356528|gb|BJ188587.1|BJ188587
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|67724058|gb|BJ974317.1|BJ974317
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|67699838|gb|BJ960071.1|BJ960071
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|18358209|gb|BJ190268.1|BJ190268
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|67709980|gb|BJ965796.1|BJ965796
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|37837576|gb|BJ595584.1|BJ595584
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|67716706|gb|BJ966966.1|BJ966966
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|67576322|gb|BJ949146.1|BJ949146
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|37833438|gb|BJ591450.1|BJ591450
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|162259896|gb|FC436031.1|FC436031
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|37827014|gb|BJ585026.1|BJ585026
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|37827815|gb|BJ585827.1|BJ585827
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|15261763|gb|BI437073.1|BI437073
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|37853590|gb|BJ611598.1|BJ611598
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|13250705|gb|BG361608.1|BG361608
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|37833460|gb|BJ591472.1|BJ591472
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|18357240|gb|BJ189299.1|BJ189299
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|37836608|gb|BJ594616.1|BJ594616
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|13251050|gb|BG361944.1|BG361944
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|67725227|gb|BJ975486.1|BJ975486
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|18339625|gb|BJ171652.1|BJ171652
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         NCAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|37841274|gb|BJ599282.1|BJ599282
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|162225990|gb|FC400995.1|FC400995
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|162224577|gb|FC400473.1|FC400473
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|18347608|gb|BJ179655.1|BJ179655
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|162225989|gb|FC400994.1|FC400994
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|67695515|gb|BJ955748.1|BJ955748
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|18356504|gb|BJ188563.1|BJ188563
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|7648252|gb|AW739235.1|AW739235
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|67709636|gb|BJ965452.1|BJ965452
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|18364186|gb|BJ196259.1|BJ196259
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAA-GG
EST: gi|67723711|gb|BJ973970.1|BJ973970
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|18360226|gb|BJ192288.1|BJ192288
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAA-GG
EST: gi|67572147|gb|BJ944971.1|BJ944971
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
EST: gi|15729024|gb|BI741098.1|BI741098
EST:     TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAG                         ACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
genomic: TCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG

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), 34 (downstream exon)
Score: 200

AAGGGAAAGCCGGATCTGCGTAAGAAGGTGATGCCTGCTGTGATCGTGCGTCAGCGCAAGCCATGGAGGCGCAAAGACGGAGTGTTCATGTACTTCGAAGgtatgcggag ... gtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggatggataattgtggagagctaacgttgagggatggtttgggtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG
                     agctaac  putative branch site (score: 200)
         ataattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaggtatgatggtgagcggggctcagatggtgttgtaggttgtggtgggatggataattgtggagagctaacgttgagggatggtttgggtttgtgcagACAATGCTGGCGTGATCGTGAATCCGAAGGGAGAAATGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA