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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttgggctaattatgtgtttatgtatttaaaagcag

Basic information

species Oryza sativa
transcript LOC_Os01g40340.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40340.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G149321_T01 (Zea mays), 5'ss of exon 9
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttg--ggctaattatgtgtttatgtatttaaaagcag
||||| |||||||||||||||||||| ||||| |||||||||||  |||| ||||||||||| |||||  ||||||||   ||||  ||  ||  | ||  | | || |||||| |||  | |  |    ||||||  | ||||| |||| ||||||
GATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAGgtaatttactatctcgaa--atgttctgtcacccttagtttttatgtgatggctgatagattatgcatgtatgtgtttataagcag

upper sequence: LOC_Os01g40340.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA15G13580.1 (Glycine max), 5'ss of exon 18
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatctta----aaacatactttggtatctttggtttttttgtccttgggctaat-tatgtgtttatgtatttaaaagcag---------------------------------------------------
||||||||||||||||||||||| ||||| || || ||||||||  ||||  |||||||||| || ||  ||||| | |||  | |      | ||||| |  ||   |||   |  |||||  |||  ||    |   || |     || |||| |                                                      
GATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAGgtaaatggtgtgcctctgttgatcatacatgtgtcaatttt-ctactttgtatttgaactgtcatgcctggtgtctcatgtaaaggtctttattccaattctttcaatgtataccttagattttgctttgacacatgcag

upper sequence: LOC_Os01g40340.2 (Oryza sativa), 5'ss of exon 16
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 5'ss of exon 18
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatt--------tgtgatcttaaaacatactttggtatctttggttt---ttttgtccttgggctaattatgtgtttatgtatttaaaagcag------------------
|||||||| |||||||||||||| ||||| ||||| ||||| ||  |||| || |||||||| |||||  ||||||         |||  | |      | |  ||  |  | ||| ||    |  | | |||| |||   | ||      |   ||   ||  |                   
GATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAGgtaatcggttcaactgttttttcctggtagaaattaat-ccgttgattcgcatcatatgcttgagcttgatgtggtcccttaacttacgaaatataacatggtgtcgttgcag

upper sequence: LOC_Os01g40340.2 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 5'ss of exon 18
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttgggctaattatgtgtttatgtatttaaaagcag-----------------------
|||||||| |||||||||||||| || || || || |||||||| |||||| ||||||||||||||||  ||||  | |    | |      || ||||   |  |   | | | ||         |||  |||     |   |   |||||||                        
GATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAGgtaggtggaagccct------tattttgaccttctccttctatatgatacctatttaaa-atgaaaaaaaaaaaaaaaaagcaatctgaaggtcttctccattgtcc

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|88694640|gb|CI738678.1|CI738678
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGCAG                       
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGAT-G--Ggtaatttgtg ... ttaaaagc
EST: gi|58691100|gb|CK079787.1|CK079787
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         TTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGGTAT
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcagTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGGTAT
EST: gi|29680847|gb|CB677122.1|CB677122
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         TTCCCTCTTTACAAATTCGAATTGGTTTACATTTGAT
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcagTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGAT
EST: gi|38473714|gb|CF957846.1|CF957846
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         TTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGGTAT
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcagTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGGTAT
EST: gi|58679221|gb|CK067908.1|CK067908
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         C
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcag-
EST: gi|58679221|gb|CK067908.1|CK067908
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         C
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcag-
EST: gi|58679221|gb|CK067908.1|CK067908
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         C
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcag-
EST: gi|58679221|gb|CK067908.1|CK067908
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         C
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcag-
EST: gi|29680806|gb|CB677081.1|CB677081
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         TTCCCTCTTTAC
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcagTTCCCTCTTTAC
EST: gi|88327344|gb|CI645125.1|CI645125
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         C
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcag-
EST: gi|88327344|gb|CI645125.1|CI645125
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         C
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcag-
EST: gi|88327344|gb|CI645125.1|CI645125
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         C
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcag-
EST: gi|88327344|gb|CI645125.1|CI645125
EST:     TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG                         C
genomic: TCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcag-
EST: gi|8956745|gb|BE230548.1|BE230548
EST:     GTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGCAG                       
genomic: GTAATATCTTCACTGCGACTGGGAGATGATCAGGAT-G--Ggtaatttgtg ... ttaaaagc

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: 71 (upstream exon), 70 (downstream exon)
Score: 20

GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtg ... ttaaaagcagTTCCCTCTTTACAAATTCGAATTGGTTTACATTTGATGGAGAGAGAGGTATTACTGACCGTTTGGCTGCGGTTCCTTCGTCTTCACCTAATTCAGAGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGgtaatttgtgatcttaaaacatactttggtatctttggtttttttgtccttgggctaattatgtgtttatgtatttaaaagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG