Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttctttttaatttttacagagtcatcttcatgtgcactttatggaagtaattaaacaccaaatgctatgttttgcttgattccatgtacttgttcattc...

Basic information

species Oryza sativa
transcript LOC_Os09g34100.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G150533_T01 (Zea mays), 5'ss of exon 1
TCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttctttttaatttttacagagtcatcttcatgtgcactt-tatggaagtaattaaacaccaaatgctatgttttgcttgattccatgtacttgttcattc
||||||||||||  | ||  |||| | |||||| || |||||||| ||||| ||||| | | | ||||| |||||||||||||||||||||||||| |||| | ||||| | ||      |   || ||||| | ||  | | | |    ||      ||   |  ||          |  | |  |||| |  ||   | 
TCATGTGTGCTATTATTTTGCTGGTTTTGGAGCTATGTTTACAGGTGACACTTTGTTCAATCTATCATGCGGAAAGCTTTTTGAAGGGACTCCACAGCAGggttttttttacttgcttgcaagtatgttcatatacatatatgttgtgcgaaggtgctactggactctcgagacaagatactcctctgtagtgcttttat-

upper sequence: LOC_Os09g34100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G120300_T01 (Zea mays), 5'ss of exon 5
TCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttt-ttaatttttacagag--tcatcttcatgtgcactttatggaagta--attaaacaccaaatgctatgttttgcttgattccatgtacttgttcattc
||||||||||||  | ||| |||| |||||||| ||||||||||| ||||| ||||| | | | ||||| |||||||||||||||||||||||||| |||||| ||   |   ||  | | |   |||| | |||||    | | || | ||   | |  ||  |   ||  |     | ||   ||  | || ||| ||  |||
TCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACACCTTGTTCAATCTATCATGCGGAAAGCTTTTTGAAGGGACTCCACAGCAGgtttttcacttgcttgcaaatatcttcatttacatgtatgttgtgtgaaggtgctactggacttc---tgtgacaagctactcctttgta-gtgctt-ttatttc

upper sequence: LOC_Os09g34100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G42070.2 (Glycine max), 5'ss of exon 5
TCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttctttttaatttttacagagtcatcttcatgtgcactttatggaagtaattaaacaccaaatgctatgtt-ttgcttgattccatgtacttgttcattc
 ||| |  ||| | | || ||||||||||| ||||| ||||| || ||||| |||||||| || |||||||| ||||| |||||||| || ||||| ||||||  |||||||| |  | |     | ||  | | |  || | ||    |  |    | | | || || ||| |||| |  |   || |   |  |  || 
CCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCAGgttggttttaattgtacctgtccttttttttttttcctttaaaggtttgagatttctatccagtgataagttgttgcatcttgggatatgtattattttt-

upper sequence: LOC_Os09g34100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G03320.1 (Glycine max), 5'ss of exon 5
TCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttctttttaatttttacagagtcatcttcatgtgcactttatggaagtaattaaa-----caccaaatgctatgtt-ttgcttgattccatgtacttgttcattc
 ||| |  ||| | | || ||||||||||| ||||| ||||| || ||||| ||||| || || |||||||| ||||| |||||||| || ||||| |||||| |||| |||| |    |     | ||| | |    ||| |   |    || |       | | | |  || ||| |||| |  ||  | || | |        
CCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTCAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCAGgttgttttaaattgtacttgtccttttttcttcttttttttcttttaaggtttgagatttctatccagtaataggttgttgcatctttggacgtgcctta------

upper sequence: LOC_Os09g34100.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 7
TCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttctttttaatttttacagagtcat-cttcatgtgcactttatgg--aagtaattaaacaccaaatgctatgttttgcttgattccatgtacttgttcattc--
 ||  |  ||| | |||| || ||||| || ||||| |||||||||||||| ||||| ||| | |||||||| || ||||| ||||| |||||  |||||||   |||| | |      |||| |   ||| ||| |  ||| ||   | |   ||||||     |   |||    |     || |||||||    ||  |    
CCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAGgtaaattttgact-----ggagttacatttcttgttctttttctgtccagggctttaaaccatctaaattatacactcaaacatgccatgtatccttttttggaa

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|29646196|gb|CB651203.1|CB651203
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|29640048|gb|CB645057.1|CB645057
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|396941317|gb|HO188526.1|HO188526
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|33682471|gb|CF310710.1|CF310710
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATG
EST: gi|8404553|gb|AU091907.1|AU091907
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGT
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACT-CCAGAAAATTATAGCACTTCCGGATGAGACAAGAGT
EST: gi|29669024|gb|CB665299.1|CB665299
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|29645268|gb|CB650275.1|CB650275
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|29645986|gb|CB650993.1|CB650993
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|29656927|gb|CB653202.1|CB653202
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|33680534|gb|CF308773.1|CF308773
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGAGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|29645569|gb|CB650576.1|CB650576
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|29663513|gb|CB659788.1|CB659788
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|29663511|gb|CB659786.1|CB659786
EST:     CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: CATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
EST: gi|58688129|gb|CK076816.1|CK076816
EST:     TTTAG-TTGTCATGTGGAAAGCTTTTTGAAAGGGACTCCACAACAG                         ATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG
genomic: TTTAGTTTGTCATGTGGAAAGCTTTTTG-AAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTG

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

TCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttcttttta ... tgtgctgcagATGTACTCTTCACTCCAGAAAATTATAGCACTTCCGGATGAGACAAGAGTGTATTGCGGACATGAATATACATTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACAGgttctttttaatttttacagagtcatcttcatgtgcactttatggaagtaattaaacaccaaatgctatgttttgcttgattccatgtacttgttcattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG