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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgtacattatccaatttgaaataaatcaatattgtgccctcatcccttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC

Basic information

species Oryza sativa
transcript LOC_Os02g31290.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------ggcaat---agcttacgttctgc--atgcggcttgtcaactttggacattg-tacattatccaatttgaa-ataaat-----caatattgtgccctcatccctt--ttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
                                              ||| ||     |||  | ||  |  ||  |||||| ||| |||| || | | || | ||||||  | ||| ||  ||     | ||  || ||  |  |  | |  |||| ||||  || ||||| || |||||||| ||||||||||||||||| |||||||||||||||||||| ||||||||||||||| |||| || |||||||| ||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagctattttttcatcgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
---------------------------------------------------ggcaatagcttacgttctgc--atgcggcttgtcaactttggacattg-tacattatccaatttgaa-ataaat---caatattgtgccctcatccc-ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
                                                      | |||| |  | ||  |  ||  | |||| ||| |||| || ||| || | |||||   ||||| ||  |    | ||  || ||| |  |  | | |||| ||||| || ||||| || |||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||| ||||||| |||||||| ||||
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 5
-------------------ggcaatagcttacgttctgcatgc--ggcttgtcaactttggacatt-gtacattatccaatttgaaataaatcaatattgtg----ccctcatcccttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
                   |   | |    |  |  |   ||     ||| | | |     |||||   |||    |  |  |    |  |  ||||   ||       | || |  || | ||||  |||| |||| ||||| ||||| || || ||||||||||||||||||||||| || |||||| | || ||||||||| ||||||| |||||||||||||
gtctgctatggaaaatgatgatgacaatcaaaatgattgctgttaaacttataatcacataacattcacacacacacacacataccctgtactaatagactgaagcttatgatgcaattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
----------------------ggcaatagcttacgttctgcatgcggcttgtcaactttggacatt-gtacattatccaatttgaaataaatcaatattgtgccctc--atcccttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
                      | ||||     | | |     |    ||| | | |     |||||   | |    |  ||    | |  |  ||||   |  | |   || | ||| | ||||  ||||||||| ||||| ||||| || || ||||||||||||||||||||||| || |||||| | || ||||||||| ||||||| |||||||||||||
gtatgctatacaaaatgatgatgacaatgaaa-atgattgctgttaaacttataatcacataacattcacagacacacgcatacacactgtactaatagactaacttatgatgcatttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgtacattatccaatttgaaataaatcaatattgtgccctcatcccttt-tttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
          |||  ||| |||   |||      ||||      ||    || |||  || | |    ||         || || |        ||  ||| | || |||||||| |||||||||||||| || || ||||| |||||| | ||| | |||||| | |||||||||||| ||||||||||||| || ||||
---------gtacagtct-catattgct-----gctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgta-cattatccaatttgaaataaatcaatattgtgccc--tcatcccttt------tttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
 | |  |||||     ||   |  |     |    | | ||   |||| |||| | |  || |||| |||  || |  | |     | |    |||      ||  ||| | ||||| || ||||| ||||||||||| ||||| ||||| |||||||| ||||| |||| | | || || |||||||||||||||||||| || ||||
-gtataagctttgtacctttttatgatcaatttg-tgtagatgatgtatcattgttct-ttagaaaaaaaggaaaaaagcgtttggttacaagtttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------------ggcaatagcttacgttctgcatgcg--gcttgtcaactttggacatt-gtacattatccaatt----tgaaataa--atcaatattgtgccctcatccctt-ttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
                                     | |   ||  | | |  | |    |||| |   ||   ||  ||  ||   | | ||| |    || | | |  |    || |  |     |||   | |||  ||| | |||||||| || |||||||| ||||| ||||||||||| |||||||| ||||| |||||| |||| ||||| ||| | |||||||||||||| ||||
gttagaatccatgcattgtaatataattatacttaatacttttttcggctttcaaaggaaagcttcttgtctacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaatgtatcatatatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgtacattatccaatttgaaataaatcaatattgtgccctcatccctt-ttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
                                           ||  |||   |    ||     |           |    ||||| |    | || ||||| |||||||| ||||||||||| ||||| ||||| ||||| || || || || ||||| ||| |||| ||||| ||    || ||  | || || ||||
------------------------------------------gtttgacaccgttgttttcttcgtg---------cgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgtacattatccaatttgaaataaatcaatattgtgccctcatcccttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
                      |     ||| ||     || |  | | ||| ||| |   ||  |   || | |   || | |  |   ||||   |||||||||||||||||||| ||||| ||||||||||| ||||| |||||||| || || || ||  | |||||||| ||  | || || || || |||||||
----------------------gttctctgtgaaa--aagagagaggagattttcctac--gacttggttctaaaacttgtcattctttgttttc-acagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC

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|58687890|gb|CK076577.1|CK076577
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
EST: gi|58691922|gb|CK080609.1|CK080609
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
EST: gi|58657140|gb|CK045820.1|CK045820
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
EST: gi|58696242|gb|CK084929.1|CK084929
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
EST: gi|56158059|gb|C72031.2|C72031
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTACCAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
EST: gi|66930475|gb|CX117323.1|CX117323
EST:     ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG                         ACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA
genomic: ATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAGgtgagagata ... ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacattatccaatttgaaataaatcaatattgtgccctcatcccttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
                              ttgtgccctcatccct  CT-rich tract
     ttatccaatttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcaatagcttacgttctgcatgcggcttgtcaactttggacattgtacattatccaatttgaaataaatcaatattgtgccctcatcccttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - -tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa