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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatacctctgctgtccatgttttgtaatcttcaattgagttgccgatattgttccgatgtttctaaatacaagttcctggcagctaacatatcataattgagctgtcagtaatctaatgtggtcttgtccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGGTTCCCACATGGTTATATCGAAAGACGAGAGCGAGTTCTAGCTAGCAAGG

Basic information

species Oryza sativa
transcript LOC_Os04g45670.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g45670.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G065176_T01 (Zea mays), 3'ss of exon 9
gtaatatacctctgctgtccatgttttgtaatcttcaattgagttgccgatattgttccgatgtttctaaatacaagttcctggcagctaacatatcataattgagctgtcagtaatctaatgtggtcttgtccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGGTTCCCACATGGTTATATCGAAAGACGAGAGCGAGTTCTAGCTAGCAAGG
                                       || |||     ||        |   || |    |  || | |    |||  | |||| || |||  |||  || |  ||   | |  |||   | ||| |||||| |||| |||||||||||||||||| ||||||||||| |||||||||||||| || |||| |||||||||||| ||||| |  |||||||| ||||| |
--------------------------------------atgggttttttttaaaaaaaaaaccatttttgccagcagctgcactaagcatatatatgatcatttggcttgcatttgtcctctcttctct---ctgaa-acagATTTCAAGCAATGGTTGGGCAGAAGGTGAATGCAAGGGCAAAGCAGGATGGTTTCCTCATGCTTATATCGAAAGGCGAGAACATGTTCTAGCAAGCAAAG

upper sequence: LOC_Os04g45670.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G104166_T01 (Zea mays), 3'ss of exon 4
gtaatatacctctgctgtccatgttttgtaatcttcaattgagttgccgatattgttccgatgtttctaaatacaagttcctggcagctaacatatcataattgagctgtcagtaatctaatgtggtcttgtccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGGTTCCCACATGGTTATATCGAAAGACGAGAGCGAGTTCTAGCTAGCAAGG
                                       || |||    | | || |   ||  || |    |  || |||    ||      ||| || |||  ||   || |  ||   | |  | |      ||||||||| |||| |||||||||||||||||| ||||||||||| ||||||||||||||||| |||| |||||||||||| |  || || |||||||| ||||| |
---------------------------------------tgggttctgtaaaatgatt-aatcatttttgccagcagctccattaagaatgtgtatgatcatttggcctgcatttgtcc--tctcttttctctgaaacacagATCTCAAGCAATGGTTGGGCAGAAGGTGAATGCAAGGGCAAAGCAGGATGGTTCCCTCATGCTTATATCGAAAGGCAGGAACGTGTTCTAGCAAGCAAAG

upper sequence: LOC_Os04g45670.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 9
gtaatatacctctgctgtccatgttttgtaatcttcaattgagttgccgatattgttccgatgtttctaaatacaagttcctggcagctaacatatcataattgagctgtcagtaatctaatgtggtcttgtccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGGTTCCCACATGGTTATATCGAAAGACGAGAGCGAGTTCTAGCTAGCAAGG
                               | ||  | |   |      |||| ||   |||||  |  ||     |  ||   | |  |  | |  ||   || ||||   | |  |  ||||  ||||        ||| | |||| || ||| ||||||||||| |||||||  ||||||||||| |||||||||  ||| || || ||||||||||| || ||||| || |||||| 
----------------------------cctttttgcagtatatcttgcttattcttagcatgtt--tggatttggttatcttttatcccagttcttttacgagatctgt---tcactttctgtg--cttg-------gcagGTGTCAAACAGTGGCTGGGCAGAAGGTGAATGCAGAGGAAAAGCAGGTTGGTTCCCAGTTGGATACATAGAAAGACGAGAACGCGTTCTTGCAAGCAAGT

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|86493211|gb|CI135844.1|CI135844
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCCAAGGGAAAAGCAGGATG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGC-AAGGGAAAAGCAGGATG
EST: gi|88549526|gb|CI479421.1|CI479421
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|88992277|gb|CI035415.1|CI035415
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCTATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|15856264|gb|BI809076.1|BI809076
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|88831791|gb|CI369473.1|CI369473
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAACCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|88472374|gb|CI409645.1|CI409645
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|88256081|gb|CI358469.1|CI358469
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|33684003|gb|CF312242.1|CF312242
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|88554670|gb|CI484862.1|CI484862
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|88838573|gb|CI375121.1|CI375121
EST:     TGAGTCTGAGCTTAACTTGTCAGGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAGAGCAGGATGG
genomic: TGAGTCTGAGCTTAACTTGTCA-GCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|88248529|gb|CI248378.1|CI248378
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|88533099|gb|CI460635.1|CI460635
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGNCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|112785829|gb|EE591501.1|EE591501
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTCATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|313081046|gb|HO213632.1|HO213632
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|88558918|gb|CI489450.1|CI489450
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|8335477|gb|BE040406.1|BE040406
EST:     GAGACATTGTTATTGGGCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|86414039|gb|CI068246.1|CI068246
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|89180460|gb|CI044739.1|CI044739
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|2276033|gb|C25010.1|C25010
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
EST: gi|88261172|gb|CI364748.1|CI364748
EST:     GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAG                         ATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG
genomic: GTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGG

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: 46 (upstream exon), 63 (downstream exon)
Score: 5

GCCCTTGATTCCTTCAAGGCTGAAAGTGAGTCTGAGCTTAACTTGTCAGCTGGAGACATTGTTATTGTCCGGAAGgtaatatacc ... ccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGGTTCCCACATGGTTATATCGAAAGACGAGAGCGAGTTCTAGCTAGCAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaacatatcataattgagctgtcagtaatctaatgtggtcttgtccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGGTTCCCACATGGTTATATCGAAAGACGAGAGCGAGTTCTAGCTAGCAAGG
                                       tcttgtcc  CT-rich tract
     atatcataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatacctctgctgtccatgttttgtaatcttcaattgagttgccgatattgttccgatgtttctaaatacaagttcctggcagctaacatatcataattgagctgtcagtaatctaatgtggtcttgtccgaacacagATATCAACCAATGGTTGGGCAGAAGGCGAATGCAAGGGAAAAGCAGGATGGTTCCCACATGGTTATATCGAAAGACGAGAGCGAGTTCTAGCTAGCAAGG

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