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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCTCAATGGTAGTTGATGGGTCCTTCGTATCGTCTATTTCTTCTGATAACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagtttattttctgcaatgtggtccattttatggttgtgcatgaactacatatttgatatatctttcctccagctcgtaatttaattctagcga...

Basic information

species Oryza sativa
transcript LOC_Os03g27019.5
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g27019.5 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G107499_T03 (Zea mays), 5'ss of exon 7
CACCTCAATGGTAGTTGATGGGTCCTTCGTATCGTCTATTTCTTCTGATAACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagtttattttctgcaatgtggtccattttatggttgtgcatgaactaca-tatttgata-tatctttcctccagctcgtaatt-taattctagcga
 || ||||||||||| ||||| || || ||||| || || || ||||||| ||| |||||||| | ||||||||| || || ||| |||| |||||||||||||    | ||| |  || |  | |  |  | | |    |   ||   |||| ||  ||     | ||     ||  ||  | || |||  || |  |    
TACTTCAATGGTAGTGGATGGCTCATTTGTATCATCCATGTCCTCTGATATCTCTGTTGAAGAAAGCAGCTTTCGACAACTGCAGAATGCTGTTAGTCAGgtatcatgggttactagcttccttttattttaatgtcccatgaagccgaaactccagcatacagcagtacagccccctcattttgttattgcaaattcat---

upper sequence: LOC_Os03g27019.5 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G093096_T04 (Zea mays), 5'ss of exon 7
CACCTCAATGGTAGTTGATGGGTCCTTCGTATCGTCTATTTCTTCTGATAACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagtttattt-tctgcaatgtggtccattttatggttgtgcatgaactacatatttgatatatctttcctccagctcgtaatttaattctagcga
 |  ||||||||||| ||||| || || ||||| ||||| || |||||||||||||| ||||| | ||||||||  || || |||||||| |||||||||||||    | ||| |  | | |  | || |   |||||   |     ||    || |  | |    ||        |   | | | ||||  || | || |
TAGTTCAATGGTAGTGGATGGCTCATTTGTATCATCTATGTCCTCTGATAACTCAGTCGAAGAAAGCAGCTTTCAACAACTGCAGGATGCTGTTAGTCAGgtatcatgggttactagttttctttttgatttcttttaatttcccatatagcataaac-tctagcctacagcagtacagccccttcattttgttattgcaa
















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|1632158|gb|C19887.1|C19887
EST:     GCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: GCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|2796328|gb|AA749622.1|AA749622
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAA-CAAAA-TGCGCAT-CGAGATGG
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGG
EST: gi|58684155|gb|CK072842.1|CK072842
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|14713831|gb|AU197793.1|AU197793
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29613852|gb|CB618865.1|CB618865
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|58655905|gb|CK044585.1|CK044585
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29627961|gb|CB632972.1|CB632972
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29626423|gb|CB631434.1|CB631434
EST:     ACTCAGTGGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29613818|gb|CB618831.1|CB618831
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29624580|gb|CB629591.1|CB629591
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|38479197|gb|CF963330.1|CF963330
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29625877|gb|CB630888.1|CB630888
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29681505|gb|CB677780.1|CB677780
EST:     AGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: AGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|218490345|gb|FG960236.1|FG960236
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCCGTTAGTCAG                         TTGGATGTGAAAACAAAACTGTGCATTCGAGCATGGGTTATACCGCCTGGC
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAG-ATGGGTTATACCGCCTGGC
EST: gi|33382007|gb|CF197350.1|CF197350
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGNGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|58678146|gb|CK066833.1|CK066833
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29630724|gb|CB635733.1|CB635733
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|56157718|gb|C25951.2|C25951
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29625284|gb|CB630295.1|CB630295
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|8857111|gb|AU094429.1|AU094429
EST:     CAGTTAGTCCG                         TTGGATGTGAAAACAAAAATGTGCATTCCGAGATGGGTTATACCGCCCTGG
genomic: CAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATT-CGAGATGGGTTATACCG-CCTGG
EST: gi|29680614|gb|CB676889.1|CB676889
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29614007|gb|CB619020.1|CB619020
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29629607|gb|CB634616.1|CB634616
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29626434|gb|CB631445.1|CB631445
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29688507|gb|CB684782.1|CB684782
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29617434|gb|CB622446.1|CB622446
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|29629983|gb|CB634992.1|CB634992
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|163928375|gb|EG712619.1|EG712619
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATT
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATT
EST: gi|29686460|gb|CB682735.1|CB682735
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
EST: gi|58686149|gb|CK074836.1|CK074836
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATA
EST: gi|29617549|gb|CB622561.1|CB622561
EST:     ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAG                         TTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA
genomic: ACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagt ... gctgtttcagTTGGATGTGAAAACAAAAATGTGCATTCGAGATGGGTTATACCGCCTGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCTCAATGGTAGTTGATGGGTCCTTCGTATCGTCTATTTCTTCTGATAACTCAGTTGAAGAGAACAGCTTTCGGCAGCTTCAGGATGCAGTTAGTCAGgtatagcagtttattttctgcaatgtggtccattttatggttgtgcatgaactacatatttgatatatctttcctccagctcgtaatttaattctagcga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG