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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagttgttcaaggtactatgtcttgcaccaacaatggagtgaaagttagtaattttactgtaaactaatgtatgttaagatatcattgaataaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG

Basic information

species Oryza sativa
transcript LOC_Os01g41870.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G480607_T02 (Zea mays), 3'ss of exon 5
cagttgttcaaggtactatgtcttgcaccaacaatggagtgaaagttagtaattttactgtaaactaatgtatgttaagatatcattgaataaat--ttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG
   |   ||    |    | | ||| |||||   |   | ||    |||| || ||    || |    |   ||||||| |||  ||  | | ||  |||||||| ||||  ||| |||||| | ||| ||||  ||||||||||||||||||| |||||||| |||||||||||  | || || ||||| || ||||| ||
ttctctctctgtttcactttttttgtaccaagggtcctgcgagc-ctagtgatgttgacatatatctgtcc-tgttaagctattttttgaaatatcattcagGTCATAATCGAGAAACATTGGAGTGGACTGCACGACAAAAGATTGCAGTTGGTGCTGCTCGTGGGCTGCGGTACCTTCACGAGGAATGTAGGGTTGGCTG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G057618_T01 (Zea mays), 3'ss of exon 4
cagttgttcaaggtactatgtctt-gcaccaacaatggagtgaaagttagtaattttactgtaaactaatgtatgttaagatatcattgaa-taaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG
|   | |       ||| | | || |  | || | |   |  ||   |||| || ||    || | |  | | ||| ||| |||  ||||| ||   |||||||||||||| ||| |||||| | ||| ||||  | || |||||||||||||| |||||||| |||||||||||  | || || ||||| || ||||| ||
cccctctctgtttcactttttttttgtgctaagagtcctgc-aagcctagtgatgttgacatatatttgtct-tgtaaagctattcttgaaatatcattcagGTCGTAATAGAGAAACATTGGAGTGGACTGCACGGCATAAGATTGCAGTTGGTGCTGCTCGTGGGCTGCGGTACCTCCACGAGGAATGTAGGGTTGGCTG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G02680.1 (Glycine max), 3'ss of exon 4
cagttgttcaaggtactatgtcttg-----caccaacaatggagtgaaagttagtaattttactgtaaactaatgtatgttaagatatcattgaataaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG
   |  |   |  ||| |||  |       ||   |  || |  |  |  ||||| ||  |    | |  |  |   ||  |   ||   ||| ||   |||||||  |  |   |||  ||||  ||||| ||||  | ||||| ||||| ||||| |||||||||||| | || ||| | |||||||| |||||||| |||||
---tcatattaaatacaatgattgaaatatcatatagtataggatacattttagtgatactggcttgatttgttaactggcatattac--ttggatgtttttcagGGAGACAGCGAGAACCATTAGAATGGACTGCCCGGCAAAAAATTGCTGTTGGAGCTGCTCGAGGGTTACGATATCTTCATGAAGAGTGCAGAGTGGGTTG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G36280.1 (Glycine max), 3'ss of exon 4
cagttgttcaaggtactatgtcttgcaccaacaatggagtgaaagttagtaattttactgtaaactaatgtatg-------ttaagatatcattgaataaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG
   || ||   |||  ||    || |||  | | || |   |||   | | ||||   |  |||  ||  ||         |||||  ||||||  |  | || |||| || ||  |  |   | || ||||||||||||| ||||||||||||||||| || ||||| ||  || | ||  | ||||||||||| ||||| |||||
---tttttattggt--taatctttacactgatagtgcatgaaaacccattgatttatatagaaaaaaaaataaaaaaacatttaagggatcatttga--atttgcagGACGAAAGCAGAATGTACTGGAATGGTCTGCTAGGCAAAAGATTGCAGTTGGAGCAGCTCGTGGCTTGAGATACCTTCATGAAGAATGTAGAGTGGGTTG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G42760.2 (Glycine max), 3'ss of exon 7
cagttgttcaaggtactatgtcttgcacca-acaatggagtgaaagttagtaattttactgtaaactaatgtatgttaagatatca-ttgaataaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG
    ||       | | || || |  |  | | | |  |  |  |   | |    | |   |    | || | |     || || | ||| ||   |||||||  |  |   |||  ||||  ||||||||||  | ||||| ||||| ||||| |||||||||||| |||| ||| | |||||||| |||||||| |||||
--aatgcaatgattgcaatatcatatagtatatagtataaagggatacattttactgatactggcttgatttgttaactgacattacttggatgtctttcagGGAGACAGCCAGAACCATTAGAATGGTCTGCCCGGCAAAAAATTGCTGTTGGAGCTGCTCGAGGGTTGCGATATCTTCATGAAGAGTGCAGAGTGGGTTG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G03340.2 (Glycine max), 3'ss of exon 3
cagttgttcaaggtactatgtcttgcaccaacaatggagtgaaagttagtaattt-tactgtaaactaat---gtatgtt-aagatatcattgaataaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG
   |  ||  |     ||    || |||  | | || | | ||| | | | |||| ||  | |||  ||    | || || |||  || |||  |  | || |||| || ||  |      | || ||||||||||||| ||||||||||||||||| || ||||| ||  || | ||  | || |||||||| ||||| |||||
---tattttgattggttaatctttacactgatagtgtattaaaactcattgatttatatagcaaaaaaaatagggatatttaagggattatttga--atttgcagGACGAAAGGAGAGCGTACTGGAATGGTCTGCTAGGCAAAAGATTGCAGTTGGAGCAGCTCGTGGCTTGAGATACCTTCACGAAGAATGTAGAGTGGGTTG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g02420.t01 (Vitis vinifera), 3'ss of exon 4
cagttgttcaaggtactatgtctt--gcaccaacaatggagtgaaagttagtaattttactgtaaactaatgtatgttaagatatcattgaataaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG
|  ||  |    |  | || | ||  |   |           |||  |||||   ||     ||    | | ||  || | ||    ||| |||  ||||||| ||  ||  |||  || |  ||||||||||| |||||||  |||| ||||| ||||||||||| ||||| ||| | ||||||||||||||||| |||||
ccattaattcttgagccattttttcagggtctttttcatgaggaagcttagtttcttcttattacttgactataaatttatatggt-ttggatac-tttcagGACGCCATCGAGATCCACTAGAATGGTCTGCTCGACAAAAAGTTGCTGTTGGAGCTGCTCGAGGTCTGCGTTATCTTCATGAAGAATGCAGAGTGGGTTG

upper sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 4
-cagttgt--tcaaggtactatgtcttgcaccaacaatggagtgaaagttagtaattttactgtaaactaatgtatgttaagatatcattgaataaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG
  |  |    ||| | | | || ||   | | |||  || | ||||   || || |  |  |||   || | | |    ||| | ||  |    || ||||||| ||| ||  ||      |  ||||||||||  ||||||| ||||||||||| |||||||||||  || | ||| | ||||||||||||||||| |||||
caaactaaagtcatgtttcaatatcc-actctaactttgtaatgaaccatactattactgttgtgg-ctga-gaaaaccaagttttctgttgggaattttcagGACGTGATCGAGGTCTGCTAGAATGGTCTGCACGACAAAAAATTGCAGTTGGAGCTGCTCGAGGATTGAGATATCTTCATGAAGAATGCAGAGTGGGTTG

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|25798254|gb|CA754215.1|CA754215
EST:     GCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATG                         GTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTG
genomic: GCTGGTCTATGAGTACATCTGCAATGGATCCTTGGATTCACATCTTTATGgtaagatcat ... taaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtaattttactgtaaactaatgtatgttaagatatcattgaataaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG
                 aactaat  putative branch site (score: 2)
                         tatgttaagatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagttgttcaaggtactatgtcttgcaccaacaatggagtgaaagttagtaattttactgtaaactaatgtatgttaagatatcattgaataaatttcagGTCGTAATAAAGAGACATTGCAATGGTCTGCTAGACAAAAGATTGCAGTTGGGGCTGCTCGAGGGCTGCGGTATTTGCATGAAGAATGCAGAGTTGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - tcttgca
- - - - - - - - - - - - - - caacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtatg