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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattaaaatgttgtaaatttgcttgcatttgtcattaacctttgcttggttcagttatctcaaattcatattttcttatcttgttttaaccatttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAAAGTGGGACAGCAAGAAAGCTCATAAATTAGTTGGAAAGACACCTTATGA

Basic information

species Oryza sativa
transcript LOC_Os10g32730.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32730.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G027115_T01 (Zea mays), 3'ss of exon 3
gtgattaaaatgttgtaaa----tttgcttgcatttgtcattaacctt----tgcttggttcagttatctcaaattcatattttcttatcttgttttaaccatttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAAAGTGGGACAGCAAGAAAGCTCATAAATTAGTTGGAAAGACACCTTATGA
|||| | |||  ||| |||    | || ||     | |  | |   ||    | ||   ||||  |||||  |  | |  ||   || ||||||     | || ||||||| | |||||||||| | ||  | ||||||||| |  | || ||||| |||| |||||| |||||||||||||| ||  ||||||| ||||||||||||||
gtgacttaaaacttggaaacaactatgattaatggttttttgaggtttagtgtactgaattcacctatct-gagctgac-ttcgattctcttgtcgactctatgtggcagATTCTGTTGTAAGTAAGGTAGTAAAACCATTTATTCTAAAGAATGGAAAAACGTGGGATAGCAAGAAAGCTCACAAGCTAGTTGGGAAGACACCTTATGA
















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|58657262|gb|CK045942.1|CK045942
EST:     GCTTATGGGGCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
EST: gi|29631920|gb|CB636929.1|CB636929
EST:     GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
EST: gi|29687643|gb|CB683918.1|CB683918
EST:     GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
EST: gi|29636237|gb|CB641246.1|CB641246
EST:     GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
EST: gi|29658982|gb|CB655257.1|CB655257
EST:     GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
EST: gi|58688816|gb|CK077503.1|CK077503
EST:     GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
EST: gi|29679504|gb|CB675779.1|CB675779
EST:     GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
EST: gi|88449572|gb|CI579852.1|CI579852
EST:     GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
EST: gi|33795313|gb|CF323528.1|CF323528
EST:     GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
EST: gi|58692132|gb|CK080819.1|CK080819
EST:     GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGT
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGT
EST: gi|29659012|gb|CB655287.1|CB655287
EST:     GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAG                         ACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA
genomic: GCTTATTTCCCATGTCATTCTTGATTTAGATGGTACCCTCTTAAACACAGgtgattaaaa ... catttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttcagttatctcaaattcatattttcttatcttgttttaaccatttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAAAGTGGGACAGCAAGAAAGCTCATAAATTAGTTGGAAAGACACCTTATGA
                                      ttttaac  putative branch site (score: 2)
                aaattcatattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattaaaatgttgtaaatttgcttgcatttgtcattaacctttgcttggttcagttatctcaaattcatattttcttatcttgttttaaccatttggcagACTGTGTTGTAAGTCAAGTGCTGAAACCATTTCTAGTCAAAAATGGGAAAAAGTGGGACAGCAAGAAAGCTCATAAATTAGTTGGAAAGACACCTTATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA