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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatctttccttgaaacaatcttttctttctgggtcttgtgacagatcacatttgagctttcctctgggtagggctttattaagatctactaacaaatgcaacaagatattcattgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC

Basic information

species Oryza sativa
transcript LOC_Os11g03730.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 13
gtgatctttccttgaaacaatcttttctttctgggtcttgtgacagatcacatttgagctttcctctgggtagggctttattaagatctactaacaaatgcaacaagatattcattgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC
                   |||| | ||||  |    |||  |        || ||| | ||  | | | | | |   | |   | |||||||    |   |  |   | || | ||| | ||    |    | ||||||||||| | ||||||||||||||||| || ||||||||||||||| ||||||| |||||
----------------gtgatctctccttttgg----ttgcaagttggttgatctgatccttattttcgttggcgggct-tggggttctactact--accaaggatagtctttactgtgagttag-atgacctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC

upper sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G006130_T03 (Zea mays), 3'ss of exon 14
gtgatctttccttgaaacaatcttttctttctgggtcttgtgacagatcacatttgagctttcctctgggtagggctttattaagatctactaacaaatgcaacaagatattcattgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC
                   |||| | ||||  |    |||  |       ||| ||| | ||  | | | | | |   | |   | |||||||    |   |  |   | || | ||| | ||    |    | ||||||||||| | ||||||||||||||||| || ||||||||||||||| ||||||| |||||
----------------gtgatctctccttttgg----ttgcaagttggttcatctgatccttattttcgttggcgggct-tggggttctactact--accaaggatagtctttactgtgagttag-atgacctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC

upper sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 14
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 14
gtgatctttccttgaaacaatcttttctttctgggtcttgtgacagatcacatttgagctttcctctgggtagggctttattaagatctactaacaaatgcaacaagatattcattgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC-
                                               |  | |||||  ||  ||        ||||||     ||||| | |  |||  || |||   | | |    ||| |||| | |  | ||||||||||  ||||| | |||||||||||||| |||||||| |||||||  |||||| | || 
----------------------------------------------gttccctttgaatttctcttc---ccaggcttt-----gatct-caactaaaaacatcaaataagtta----aacatcttat-gactttttgcagTGACATTGTTGAAATGGCAAGTTATGCTCCACTCTTTGTGAACACAAATGAT-AGACG

upper sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 15
gtgatctttccttgaaacaatcttttctttctgggtcttgtgacagatcacatttgagctttcctctgggtagggcttta--ttaagatctactaacaaatgcaacaagatattcattgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC
                                           |   |  |||||      |  | |  ||    |||    ||    | || |     | || |||  |  | |   |||  | |||  || | |  ||||||||||||||| |||||||||| ||||||||||| || |||||   ||||||    ||
-------------------------------------------ccattatcatttatctcctgttttttgtgatccttatgcttttagtttagttttggaagctacagtagttaccgggtacttactttctgctccaatgcagTGATGTTGTTGAGATGGCAAGCTATGCACCACTTTTTGTGAATTCCAATGACAGGAC

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|29665627|gb|CB661902.1|CB661902
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|29636384|gb|CB641393.1|CB641393
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|29674665|gb|CB670940.1|CB670940
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|29677794|gb|CB674069.1|CB674069
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|87021358|gb|CI295417.1|CI295417
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|29627661|gb|CB632672.1|CB632672
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|29624426|gb|CB629437.1|CB629437
EST:     CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|33795281|gb|CF323512.1|CF323512
EST:     CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATG
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTG-ATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATG
EST: gi|29646542|gb|CB651549.1|CB651549
EST:     CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|29628284|gb|CB633295.1|CB633295
EST:     CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|86905528|gb|CI285491.1|CI285491
EST:     CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|29624428|gb|CB629439.1|CB629439
EST:     CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|29627934|gb|CB632945.1|CB632945
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|29644766|gb|CB649773.1|CB649773
EST:     CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
EST: gi|29638132|gb|CB643141.1|CB643141
EST:     CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGA

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: 65 (upstream exon), 57 (downstream exon)
Score: 43

TTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAGGCAGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctactaacaaatgcaacaagatattcattgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC
                                             ttctttgc  CT-rich tract
                     atattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatctttccttgaaacaatcttttctttctgggtcttgtgacagatcacatttgagctttcctctgggtagggctttattaagatctactaacaaatgcaacaagatattcattgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG