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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggaactatcgagtccctcacttccgattttagcttagagtgagtttgcttgttcttactgtagacactgataatgtatcgattcaacgctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTAGCTACAGGCGGAGGAGGAGGGACCACTGGAGGAATGC

Basic information

species Oryza sativa
transcript LOC_Os01g74640.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74640.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 1
taggaactatcgagtccctcacttccgattttagcttagagtgagtttgcttgttcttactgtagacactgataatgtatcgatt---caacgctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTA--GCTACAGGCGGAGGAGG-AGGGACCACTGGAGGAATGC
|   || ||  ||||   | | |      | ||    ||| ||  | |   |||      | | |     ||    |  | ||||   ||| | | | |||||||||||||||||||| | |||||||||||||||||||| |||||||||| ||| ||  | |||  ||| |   ||| ||  | ||   |||| |  |      
ttaaaaatag-gagta--tgattatttgatctaaaaaagaatggatctcactgtcaacgatttgggtttggagccagctttgatttaccaatgatataatcagGTGTGCACCATTCCTTTGGACACAGCCAAAGTGCGGCTCCAGCTGCAAAGGAAGGCGCCACTACCGCTGCCACCGGCGGCTGCAGCAGCCACAGCTGCTG---

upper sequence: LOC_Os01g74640.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G852877_T02 (Zea mays), 3'ss of exon 1
---------taggaactatcgagtccctcacttccgattttagcttagagtgagtttgcttgttcttactgtagacactgataatgtatcgattcaacgctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTA--GCTACAGGCGGAGGAGG-AGGGACCACTGGAGGAATGC
          || || ||    |    | | ||  ||| | ||     |||  ||   |   ||     || || ||    | || || |     |  | | | |||||||||||||||||||| | |||||||||||||||||||| |||||||||| ||| ||| | |||  |   |   | | ||  | ||   |  |||  |||    
gcttcttcaaagaaagtaggacgatgtttattt--gatctcagacacaagt--gtcaacgattttggcttggagtcagctttgatttacc-----agtgatataatcagGTGTGCACCATTCCTTTGGACACAGCCAAAGTGCGGCTCCAGCTGCAAAGGAAGGCACCACTACCGTCGCCACCAGTGGCTGCAGCAGCTGCTGCTGGAG---

upper sequence: LOC_Os01g74640.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 1
taggaactatcgagtccctcacttccgattttagcttaga-gtgagtttgcttgttcttactgtagacactgataatgtatcgattcaacgctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTA-----GCTACAGGCGGAGG-AGGAGGGACCACTGGAGGAATGC-------------------
                           |||| | || |||    ||| |    | | ||    | ||  | | |  |  ||  |  ||  | | | |||||||||||||||||||| | |||||||||||||||||||| |||||||||| ||| ||| | |||     || ||  | ||  | || ||   |  ||||||| | ||                   
-----------------------gtttatttgatctcagacacaagtgtcaacgattttggcttggagtcagct--ttgatttac-cagtgatataatcaggtgtgcaccattcctttggacacagCCAAAGTGCGGCTCCAGCTGCAAAGGAAGGCACCACTACCGTCGCCACCAGTGGCTGCAGCAGCTGCTGCTGGAGGCACGCTAGCCACAATCATGTGCAT

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|58655848|gb|CK044528.1|CK044528
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88766139|gb|CI775229.1|CI775229
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88692659|gb|CI736234.1|CI736234
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88724279|gb|CI747538.1|CI747538
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88305150|gb|CI652088.1|CI652088
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88352327|gb|CI615581.1|CI615581
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|33795983|gb|CF323859.1|CF323859
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|86905823|gb|CI290957.1|CI290957
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88375556|gb|CI681339.1|CI681339
EST:     CCTTCGCCGNCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88745080|gb|CI768440.1|CI768440
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88730203|gb|CI753818.1|CI753818
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88335568|gb|CI642792.1|CI642792
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88288360|gb|CI661565.1|CI661565
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88694449|gb|CI738487.1|CI738487
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88732454|gb|CI755631.1|CI755631
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88442656|gb|CI693657.1|CI693657
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGANACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
EST: gi|88342848|gb|CI640181.1|CI640181
EST:     CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAG                         GTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG
genomic: CCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAG

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: 74 (upstream exon), 65 (downstream exon)
Score: 6

CTAGGAAGTCGCCTCCGCCTCCGCTGCAGACACACTGGCGATGGCTTCCTCCTTCGCCGCCGTCTTCTTCAGCAGCGCCTTCGCTGCCTGCTTCGCTGAGgtaagcacgc ... ctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTAGCTACAGGCGGAGGAGGAGGGACCACTGGAGGAATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcttgttcttactgtagacactgataatgtatcgattcaacgctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTAGCTACAGGCGGAGGAGGAGGGACCACTGGAGGAATGC
                                             ctctcatc  CT-rich tract
                          ataatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggaactatcgagtccctcacttccgattttagcttagagtgagtttgcttgttcttactgtagacactgataatgtatcgattcaacgctctcatcagGTGTGCACCATTCCTCTCGACACAGCCAAAGTGCGGCTTCAGCTGCAAAAGAAAGCAGCCCTAGCTACAGGCGGAGGAGGAGGGACCACTGGAGGAATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA