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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatcacatcgattgaaatgaagtatgttttgtggtgttattacttatgaacattatttcatgtttaagttagtactaataagtgattttgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA

Basic information

species Oryza sativa
transcript LOC_Os03g57790.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G007260_T03 (Zea mays), 3'ss of exon 2
aaaatcacatcgattgaaatgaagtatgtttt--gtggtgttattacttatgaacatt---atttcatgtttaagttagtactaataagtgattttgtcac--atagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA
       | | | |         || | || |  |  |    |  |    |   | ||   |||| |  | | |||| |     ||| || |  ||  |||   ||||||||||||||||||| || ||||||||||||||||| ||||||||||| ||   |||||||||||| || ||||||||||||||||| |
-------cgtggttcacctcagtgtcttttattggcagcagaacaaaccgtctgctttctgattttaactgtcagtttgctaacatatgtcaagtttacacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA

upper sequence: LOC_Os03g57790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G007260_T01 (Zea mays), 3'ss of exon 3
---------aaaatcacatcgattgaaatgaagtatgttttgt-ggtgttattacttatgaacattatttcatgtttaa--gttagt--actaataagtg----attttgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA
         |  || | |     |  |    ||| | |||| | ||    |  ||  |    |    ||     |||||  || |||   |||| |  ||     |||   |   ||||||||||||||||||| || ||||||||||||||||| ||||||||||| ||   |||||||||||| || ||||||||||||||||| |
gtatgctataccattagacgtggttcacctcagtgtcttttattggcagcagaacaaaccgtctgctttctgattttaactgtcagtttgctaacatatgtcaagtttacacttgtagGCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACA

upper sequence: LOC_Os03g57790.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G120674_T01 (Zea mays), 3'ss of exon 2
aaaatcacatcgattgaaatgaagtatgttttgtggtgttattacttatgaacatt---atttcatgtttaagttagtactaataagtgattttgtcac--atagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA
      |||| | |    |     | |  || |  |    |  |  |     | ||   |||| |  | | |||| |      || || |  ||  |||   ||||||||||||||||||| || |||| |||||||||||| ||||||||||| |||  |||||||||||| || ||||||||||| ||||| |
-----gacatggttcatcagtgtcttttattggcagcagaacaaactggctgctttctgattttaactgtcagtttgctaacgtatgtcaagtttacacttgtagGCACGTTCAAGCTGACTCTGCAATGTACAGAAGATTACCCCAACAAACCTCCAACTGTTCGGTTTGTTTCGAGGATGTTTCATCCAAACA

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|11025772|gb|AU162373.1|AU162373
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|88220568|gb|CI220128.1|CI220128
EST:     CATATTCGGACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: CATATTCGGACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|58688873|gb|CK077560.1|CK077560
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|38469192|gb|CF953323.1|CF953323
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCGCGAACAAACC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCC-C-AACAAACC
EST: gi|4716198|gb|AU057314.1|AU057314
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|38468844|gb|CF952975.1|CF952975
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|218505167|gb|FG956727.1|FG956727
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|38469613|gb|CF953744.1|CF953744
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|58590675|gb|CF988983.1|CF988983
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|42592241|gb|CK738727.1|CK738727
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|218485740|gb|FG958740.1|FG958740
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|27576883|gb|CA999577.1|CA999577
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|38468296|gb|CF952427.1|CF952427
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|38474625|gb|CF958758.1|CF958758
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|86419732|gb|CI054533.1|CI054533
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|38480664|gb|CF964753.1|CF964753
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|87030448|gb|CI252725.1|CI252725
EST:     TCATATTCGGACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: TCATATTCGGACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|58677295|gb|CK065982.1|CK065982
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|29666285|gb|CB662560.1|CB662560
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|33797775|gb|CF324747.1|CF324747
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
EST: gi|218500669|gb|FG957555.1|FG957555
EST:     ACCGGATGACACGCCGTGGGATGGAG                         GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC
genomic: ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCAC

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: 43 (upstream exon), 50 (downstream exon)
Score: 6

ACCGGATGACACGCCGTGGGATGGAGgtgagtccat ... tgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgaacattatttcatgtttaagttagtactaataagtgattttgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA
                             tactaat  putative branch site (score: 6)
                                          ttttgtc  putative PPT
        attatttcatgtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatcacatcgattgaaatgaagtatgttttgtggtgttattacttatgaacattatttcatgtttaagttagtactaataagtgattttgtcacatagGCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG