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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacaaatgttcaaaataaacatgaaatatacattcagttatttcgtactatgttgttttatcatgttatttacctgtcatctctatccacatggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGATATTGTTGGACCAGTTTGTGAATCTGCAGATTTCCTTGGCAAAGACAGGG

Basic information

species Oryza sativa
transcript LOC_Os02g24354.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G020446_T01 (Zea mays), 3'ss of exon 5
-----caacaaatgttcaaaataa-acatgaaatatacattcagttatttcgtactatgttgttttatcatgttatttacctgtcatctctatccacatggtgcagCATATCGAACTGGTTTCTCCTTCC---CCAGATGCAGAAGTAGCAACATTCGATATTGTTGGACCAGTTTGTGAATCTGCAGATTTCCTTGGCAAAGACAGGG
     |   |||||   | || |  |  | || |  | |  ||   || || ||| | |        | || | |  |       ||   ||  ||  ||  |||||||||||||||||| |||||  ||   || | ||| |||| ||| || |||||||||||||||||||||||||| ||||||||||||||||| ||||| |   
gtttccttgaaatgcatagaaaatcatgttaactgcataaacaaaaatgtcatacaaagaaa----gttatttcagctcttgaatattgttactcatgtg--gcagCATATCGAACTGGTCTCTCCCCCCACTCCTGGTGCTGAAGCAGCGACCTTCGATATTGTTGGACCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA---

upper sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G090722_T02 (Zea mays), 3'ss of exon 5
caacaaatgttcaaaataaacatgaaatatacattcagttatttcgtactatgttgttttatcatg----ttattt-acctgtca--tctctatccacatggtgcagCATATCGAACTGGTTTCTCCTTCC---CCAGATGCAGAAGTAGCAACATTCGATATTGTTGGACCAGTTTGTGAATCTGCAGATTTCCTTGGCAAAGACAGGG
       |  |  ||||    |  ||||  |  || |          || |  ||||  |   | |    |||||| | |||| |  |||   | | ||||  ||||||||||||| |||| |||||  ||   || | ||| |||||||| || |||||||||||||| ||||||||||| ||||||||||||||||| ||||| |   
------ttcattgaaatgcgtagaaaat-catgttaacactgcataaacaaaattgtcatgcgaagaaagttattttagctgttaaatcttgttactcatgtggcagCATATCGAATTGGTCTCTCCCCCCACTCCTGGTGCTGAAGTAGCGACCTTCGATATTGTTGGGCCAGTTTGTGAGTCTGCAGATTTCCTTGGAAAAGATA---

upper sequence: LOC_Os02g24354.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G06090.1 (Glycine max), 3'ss of exon 9
caacaaatgttcaaaataaacatgaaatatacattcagttatttcgtact---atgttgttttatcatgttatttacctgtcatctctatccacatggtgcagCATATCGAACTGGTTTCTCCTTCCCCAG---ATGCAGAAGTAGCAACATTCGATATTGTTGGACCAGTTTGTGAATCTGCAGATTTCCTTGGCAAAGACAGGG
| |    || |   | | || |||  || |   ||  | | |||  || |   |  ||  |||  | ||    ||   || ||| ||  |      | |||||||||||||||||||||| ||| ||||||   |||| ||  ||||||  || ||| || |||| || || ||||| |||||||||||| |||| ||||| |   
ccatttctgatgttactcaa-atgccatttg-gttgtgcttttttatattcagaaatttcttttccttgaatattgaatgacatgtc-gttgtttcgttgcagCATATCGAACTGGTTTCCCCTGCCCCAGCAGATGCTGAGATAGCAAAGTTTGATGTTCTTGGTCCTGTCTGTGAGTCTGCAGATTTCTTTGGAAAAGATA---

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|58607496|gb|CK035529.1|CK035529
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|87029427|gb|CI250360.1|CI250360
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|29617055|gb|CB622067.1|CB622067
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|88246474|gb|CI246323.1|CI246323
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|88846086|gb|CI372854.1|CI372854
EST:     CAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: CAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|300215949|gb|HO088575.1|HO088575
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTC
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTC
EST: gi|86504611|gb|CI147244.1|CI147244
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|32948069|gb|BP184641.1|BP184641
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|29678833|gb|CB675108.1|CB675108
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|29646003|gb|CB651010.1|CB651010
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|218503477|gb|FG956525.1|FG956525
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|86497107|gb|CI139740.1|CI139740
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
EST: gi|29615943|gb|CB620955.1|CB620955
EST:     ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAG                         CATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT
genomic: ATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGAT

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: 71 (upstream exon), 71 (downstream exon)
Score: 35

TAGGGTCACTGGTGTTAAATCTAATGGTACAAAGAATTTCATTGTAGTTGATGGCAGCATGGCAGAGCTTATCAGACCAAGTCTATATGGAGCATACCAGgtttgtttag ... catggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGATATTGTTGGACCAGTTTGTGAATCTGCAGATTTCCTTGGCAAAGACAGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactatgttgttttatcatgttatttacctgtcatctctatccacatggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGATATTGTTGGACCAGTTTGTGAATCTGCAGATTTCCTTGGCAAAGACAGGG
           ttttatcatgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacaaatgttcaaaataaacatgaaatatacattcagttatttcgtactatgttgttttatcatgttatttacctgtcatctctatccacatggtgcagCATATCGAACTGGTTTCTCCTTCCCCAGATGCAGAAGTAGCAACATTCGATATTGTTGGACCAGTTTGTGAATCTGCAGATTTCCTTGGCAAAGACAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
caacaaa
- - - - - - -aaataaa
- - - - - - - - - - catgaaa
- - - - - - - - - - - - - - - -cattcag
- - - - - - - - - - - - - - - - - - - - - - - - - atgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgtca