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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttatattagtatcacccttaaatattctattgtcattattatgcatgtgtttgagccgcttccatttttaattatactggtagagttgtagtttcctcttctttaaactgctacttaataatccactctttttactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG

Basic information

species Oryza sativa
transcript LOC_Os02g41590.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 2
gtaagtatttatattagtatcacccttaaatattctattgtcattattatgcatgtgtt------------tgagccgcttccatttttaatt------------atactggtagagttgtagtttcctcttctttaaactgct-acttaataatccactctttttactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
|||||||| | ||| | |    |   |  ||||   ||| |  || | ||| || | ||            ||||  | |  |  ||| ||||            ||| | | |      || | |    |  |  |  ||| | |  |||||||    | | |||  ||  ||||||||| |||||||| |||||| ||||||||||||||||||||||||
gtaagtatatgtatcactgatgctactttatatgtcattattttt-tcatgtattttttgttgctgaactttgagttgttgtctatttaaatttactgagaagacatatttgcattccaatactgtgtcttgttgcatgctgtttatctaataataaggtgtgtttttttgacagGTATGACGAGTTGGCTAGCAAGAGCAATGTTGAATATATTGCCGGAG

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 2
gtaagtatttatattagtatcacccttaaatattctattgtcattattatgcatg-tgtttgagccgcttccatttttaattatactggtagagttgtagtttcctcttctttaaactgct-acttaataatccactctttttactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
                                                 |||| | ||           |  | |   ||  | | | | |   |  || ||     | || ||  ||| | |  |||||||    |   |||  ||  |||||||||||||||||| |||||  ||||||||||||||||||| ||||
-------------------------------------------------tgcaagctgcacactttaactttactgagaag-acatttgcattctaatacttcgtcttgctgtatgctgtttatctaataataaggtgcgttt--ttgacagGTATGATGAGTTGGCTAGCAACAGCAATGTTGAATATATTGCTGGAG
















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|84117280|gb|CD151047.1|CD151047
EST:     TGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGGGGTGTTGAATATATTGCCGGAG
genomic: TGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
EST: gi|428330|gb|D24478.1|D24478
EST:     GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
genomic: GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
EST: gi|58598930|gb|CK009458.1|CK009458
EST:     TGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
genomic: TGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
EST: gi|163918496|gb|EG710298.1|EG710298
EST:     GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
genomic: GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
EST: gi|428228|gb|D24376.1|D24376
EST:     GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
genomic: GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
EST: gi|88719065|gb|CI742575.1|CI742575
EST:     TGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
genomic: TGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
EST: gi|88733084|gb|CI756261.1|CI756261
EST:     GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
genomic: GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
EST: gi|88394239|gb|CI603428.1|CI603428
EST:     GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
genomic: GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
EST: gi|66922324|gb|CX109172.1|CX109172
EST:     GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
genomic: GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
EST: gi|55410432|gb|CV722808.1|CV722808
EST:     GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
genomic: GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
EST: gi|33820427|gb|CF336024.1|CF336024
EST:     GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTT
genomic: GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTT
EST: gi|58657974|gb|CK046654.1|CK046654
EST:     GACGTCAAGCTGAACAATGCAATGCGCGCTGAGGAAAAGCACTTGCCTAT                         GTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
genomic: GACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG

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: 61 (upstream exon), 75 (downstream exon)
Score: 114

GTATGACGTCAAGCTGAACAATGCAATTCTCGCTGAGGAAAAGCACTTGCCTATgtaagtattt ... tactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagtttcctcttctttaaactgctacttaataatccactctttttactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG
                         acttaat  putative branch site (score: 114)
                                  tccactctttttactt  putative PPT
                        tacttaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatttatattagtatcacccttaaatattctattgtcattattatgcatgtgtttgagccgcttccatttttaattatactggtagagttgtagtttcctcttctttaaactgctacttaataatccactctttttactttgcagGTATGATGAGTTGGCCAGCAAGGGCAATGTTGAATATATTGCCGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG