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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 25
gtaaagcgattatatgattgtactgcttattgatgttattttt-ccttttttattttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
|||||   |  |||  || |  |     | |  ||  |||  |  |  |     |||   || |||| |   ||     |||   |||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||| || ||||| || |||||||||||||
gtaaaataaaaataaaatag--ccagacagtcgtgcaattcctgtcgctaccgcttttaatttaatagcatgtgtt---aatttattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
--gtaaagcgattatatgattgtactgcttattgatgttatttt----------tccttttttattttattttgaat--aactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
    ||| |    | |||   | | ||| ||||| |||| || |          | ||| ||  |  | |||| |||  || ||   |     ||  ||||| ||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| || || |||||||| |
gtacaaaacagccagatg--cgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 11
gtaaagcgattatatgattgtactgcttattgatgttattttt-ccttttttattttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
|||||   |  |||  || |  |     | |  ||  |||  |  |  |     |||   || ||||||   ||     |||   |||| |||||| |||||||||||||||| ||||||||||||||||| |||||||||||||||||||||| ||| |||||||| || ||||| || |||||||||||||
gtaaaataaaaataaaatag--ccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgtt---aatttattgagcagCTTCAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGACAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 11
gtaaagcgattatatgattgtactgcttattgatgttattttt-ccttttttattttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
|||||   |  |||  || |  |     | |  ||  |||  |  |  |     |||   || ||||||   ||     |||   |||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||| || ||||| || |||||||||||||
gtaaaataaaaataaaatag--ccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgtt---aatttattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 3
--gtaaagcgattatatgat--tgtactgcttattgatgttatttttcct------------------tttttattttattttgaataactaatggctgga-atgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
    |||      | || ||  || | ||| ||||| || |  | ||  |                  || ||| |   |||| | | | |||    ||   ||  || || ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| || || |||||||| |
gtacaaaatagccagataatcttgcagtgcctattgctgctgctgttgttgtaatcgtgcgatgcatattgttactgctttttaatttaataacctgtgtccatttctggagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 6
gtaaagcgattatatgattgtactgcttattgatgttattttt-ccttttttattttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
|||||   |  |||  || |  |     | |  ||  |||  |  |  |     |||   || ||||||   ||     |||   |||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||| || ||||| || |||||||||||||
gtaaaataaaaataaaatag--ccagacagtcgtgcaattcctatcgctaccgcttttaatttaataacatgtgtt---aatttattgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 26
---------gtaaagcgattatatgattgtactgctta-------ttgatgttatttttccttttttattttat----tttgaataactaatggctgg-------aatgc-cttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
             | |  || | | ||| |     |||       | ||  | |   |    |    | ||||     ||||||| | || ||  |||       ||| | | ||| ||| |||||||||||||| | |||||||||||| |  | |||||||||||||||||||| || || |||||||||||||| |||||  |||| ||||||||||
gtgaatcttacttatcttttgtcttattttgacaattagcaaaaatcgagatcagaatgttatgggaaatttaaaatatttgaattattattgattggcttcaacaatacacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTTGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 25
gtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaatgg-ctggaatgccttgat---cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
              |   || | |  || || |||||   | |  ||||   ||  ||| |    ||| | |||  |   ||   |||     ||| |||| ||||||||  | |||||||||||  |  ||||||| || |||||||||||||| || |||||||| || || |||||| |||| |||||||| |
------------gttagctgcatttattcttcatgttgactat--ttttcagttcaattataggaaaccagtggattattattatttggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 24
-----gtaa--agcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaatggctggaatgcct-tgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
     ||||  ||   | |    ||   ||   || || |    |   |  | ||    ||| |   | | | | |         ||||  | ||  ||| |||||||||||||  | |||||||||||| |  | ||||| |||||||| ||||| ||||| ||||||||||| || |||||  |||| || |||||||
tttttgtaattagaagtgaagacataaaacattttgttaaaccaagcatagccttaaagtttgacaattagtgattggctttaacaatgtgtatgtgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTTGCTGCTTACATTTATAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
-gtaaagcgattata--tgattgtactgcttattgatgttatttttccttttttattttattttga--ataactaatggctggaatgccttg-at---cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
  |   |  |||| |  |||    |    | |||  |||||         |    ||  | |||||  ||   |  |||||  ||     || ||   ||| |||||||||||||  | |||||||||||| |  ||||||| || ||||||||||| ||||| ||||||||||| || |||||  |||| || |||||||
atttttgtaattaaaagtgaagtcagaaatcattt-tgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 26
---------gtaaagcgattatatgattgtactgctta-------ttgatgttatttttccttttttattttat----tttgaataactaatggctgg----aatgc--cttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
         |   | |  || | | ||| |     |||        |||  | |        |    | ||||     ||||||| | || ||  |||    ||     | ||| ||| |||||||||||||| | |||||||||||| |  | |||||||||||||||||||| || || |||||||||||||| |||||  |||| ||||||||||
gtgaatctcggttatcttttgtcttattttgacaattagcaaaatctgagatcaggaagttatggaaaatttaaaatgtttgaattattattgattggcttcaacaatacatgagcagATTGAGAAGCATGAACTTCTTGAGATGAGGCGTGTAGCTGCCTACATTTACAAGAAAGCAGGAAGATGGAAGCAATCCATTGCTTTGTCAAAGAAAGACA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
gtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaatggctgg-----aatgccttgat--cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
              ||  || | |  || || |||||   |    ||||| | || ||| |    |||  || | |       | |  || ||   ||| |||| ||||||||  | |||||||||||  |  | ||||| || |||||||||||||| || ||||||||||| || |||||| |||| ||||| || |
------------gttggctgcattcattcttcatgttgacta---tttttcagttaattataggaaaccgatagattattattattatctggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
gtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaa--tggctggaatgc-cttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
||  ||  || || |  ||    |||  |||| | || ||| |  || | |    |  ||    | |  |   | | ||| |||   |||| ||| ||||||| || ||  | |||||||||||  |  | ||||| || ||||||||||| || ||||||||||||||||| |||||  |||||||||||||||
gtggagt-ataatttcttta-ggtgca-attgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA

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|12622957|gb|AU173170.1|AU173170
EST:     AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAG                         CTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
genomic: AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
EST: gi|5005228|gb|AU070390.1|AU070390
EST:     AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAGAAG                         CTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
genomic: AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
EST: gi|29685119|gb|CB681394.1|CB681394
EST:     AATCGGTTGATATGCATGACAACTTTGATCATATAGGTCTTGCCCAGAAG                         CTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
genomic: AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
EST: gi|29664581|gb|CB660856.1|CB660856
EST:     AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAG                         CTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
genomic: AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
EST: gi|87017011|gb|CI286147.1|CI286147
EST:     AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAG                         CTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC
genomic: AATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTAC

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), 75 (downstream exon)
Score: 106

AGCTTTGAATGAGCTTTATGTTGAAGAGGAGGACTATGAGAGACTCCGTGAATCGGTTGATATGCATGACAACTTTGATCAGATAGGTCTTGCCCAAAAGgtaaagcgat ... ccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttccttttttattttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA
                            aactaat  putative branch site (score: 106)
     tccttttttattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaatggctggaatgccttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA