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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaacatcgaaatttctacaatatgtttatgcccttctctaacaaattcccttatgtaatttgtgcagcatcttacacaaattgttatgatttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAGATGGCAGATATTACAGAAGAAGGGGTTTCAT

Basic information

species Oryza sativa
transcript LOC_Os02g25580.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g25580.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 2
aaaacatcgaaatttctacaat-atgtttatgcccttctctaacaaattcccttatgtaatttgtgcagcatctta--cacaaattgttatgatttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAGATGGCAGATATTACAGAAGAAGGGGTTTCAT
   |      ||||   ||| |  | ||  | || || | ||| ||||   | |   |  ||| |   |||| |||  ||||||||||||||||  ||||||||||||||| ||||||||  ||||||||||||| || |||| | ||||||||||||||||||||||||||||||| |||||||
---atgagataattgtaacatttgttttcctcccattttataataaatattcctgcatttttttttttgcattttattcacaaattgttatgatggcttctagGTTCTTATCATGGATAAGTTTACAGTCAAGATTATGTCATATGCATGTAAGATGGCAGATATTACAGAAGAAGGTGTTTCAT
















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|88744212|gb|CI767572.1|CI767572
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGG
EST: gi|29689434|gb|CB685709.1|CB685709
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88420813|gb|CI564649.1|CI564649
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|58691232|gb|CK079919.1|CK079919
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88391359|gb|CI598177.1|CI598177
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|29634393|gb|CB639402.1|CB639402
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|33794771|gb|CF323265.1|CF323265
EST:     ATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACCATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAA
genomic: ATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAAC-ATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAA
EST: gi|88367594|gb|CI568366.1|CI568366
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAAAATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|58611429|gb|CK039141.1|CK039141
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88387048|gb|CI577834.1|CI577834
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88415404|gb|CI586610.1|CI586610
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|58687532|gb|CK076219.1|CK076219
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88394991|gb|CI607718.1|CI607718
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88574709|gb|CI666478.1|CI666478
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88325728|gb|CI648173.1|CI648173
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88730327|gb|CI753941.1|CI753941
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTCCATGTAA
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAA
EST: gi|117231551|gb|CT846912.1|CT846912
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88311860|gb|CI577466.1|CI577466
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88324396|gb|CI566209.1|CI566209
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCA-GATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
EST: gi|88294730|gb|CI604602.1|CI604602
EST:     TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAG                         GTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG
genomic: TATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAG

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: 69 (upstream exon), 75 (downstream exon)
Score: 8

GTTTATTATTTGAAATGCTCAGGTCAACTAGGAAACATTCAAAATCAACATGGAAGgtaaggaatc ... tttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAGATGGCAGATATTACAGAAGAAGGGGTTTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcccttatgtaatttgtgcagcatcttacacaaattgttatgatttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAGATGGCAGATATTACAGAAGAAGGGGTTTCAT
                        atcttac  putative branch site (score: 8)
                                             tttcttct  putative PPT
                                 aaattgttatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaacatcgaaatttctacaatatgtttatgcccttctctaacaaattcccttatgtaatttgtgcagcatcttacacaaattgttatgatttcttctagGTTCTTATTATGGATAAACTTACAGTCAAGATAATATCATGTTCATGTAAGATGGCAGATATTACAGAAGAAGGGGTTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
-aaacatc
- - - - - - - - - - - - - -tatgccc
- - - - - - - - - - - - - - - - - - - -taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg