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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctggatgctaatatctgtttagaaatagcatttccaaagtaaccgttcaataatgatgtgaactgtttgttcctgcag

Basic information

species Oryza sativa
transcript LOC_Os03g51650.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g51650.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G149576_T01 (Zea mays), 5'ss of exon 10
GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctggatgctaatatctgtttagaaatagcatttccaaagtaaccg--ttcaataatgatgtgaactgtttgttcctgcag---------------
|| |||||||||||||||||||||||||||||||||||||| ||||| || || |||||||| ||||||||| ||||||||||  | ||||||||||| |||  | |   ||| ||||   ||  |      || |   | ||  |  ||| ||  | ||    |   |||   |    |                
GTGGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCCTCCCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccatgttagaaatctctga--agccacgtttgtttcgttgaaattgaattctattctaataatcataatttaaacacaaactaattaagttaatat

upper sequence: LOC_Os03g51650.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT2G36630.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaat-tcctggatgc------taatatctgtttagaaatagcatttccaaagtaaccgttcaataatgatgtgaactgtttgttcctg-cag
||||| || |||||||| || || ||||||||||| || || ||| |||||||||| ||||||||  |||| || ||||||||||| || |  |||||  ||    |  |      | | ||   ||||||| | | |   |  ||  ||  |   | | ||||| ||| || | | |   || |||
GTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCCGTAGTCGAGTTCTATCTCCTCAAGAGATTCCCAATACCATACGgtaagatctctaacacacaacatgagatacatttagaagtcgtag--cagaataaaaaggaaactgatgat-tgacctttgtttcattgacag

upper sequence: LOC_Os03g51650.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv08s0007g04230.t01 (Vitis vinifera), 5'ss of exon 10
GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctggatgctaatatctgtttagaaatagcatttccaaagtaaccgttcaataatgatgt-gaactgtttgttcctgcag-----------------------
|||||||| || |||||||| || |||||||||||||| |||||| |||| || |||||||||||| |||| || || || || || || | ||||| |||       || ||   | |  ||   |   |||| || |   |   ||||  || |   |  || ||   ||   | ||                        
GTTGCAAGCGCGACAGCAACTTTTGTGATGATGTTCTCATCATCCTTATCTGTTGTGGAGTTCTACCTCCTCAAGAGGTTTCCCATTCCATATGgtagttct------cttatccatctccagggctttgattttcaga---atttttcataaacggcttcaaattgggcgtgttttcattgaaacgagatttatcttagtga

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|86478929|gb|CI121562.1|CI121562
EST:     TCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: TCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|29669369|gb|CB665644.1|CB665644
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|87030251|gb|CI270261.1|CI270261
EST:     TTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: TTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|58598328|gb|CK008856.1|CK008856
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|4715479|gb|AU056596.1|AU056596
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGC-AGTCCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|4715480|gb|AU056597.1|AU056597
EST:     ACAGATTCCCAAANCCCTTTTG                         CTGTCTACCTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCC
genomic: ACAGATTCCC-AATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTA-CTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCC
EST: gi|86502892|gb|CI145525.1|CI145525
EST:     TATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: TATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|87021173|gb|CI271980.1|CI271980
EST:     CCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: CCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|25803688|gb|CA759649.1|CA759649
EST:     TCCCAAATCCCTTTTG                         CTGTCTACTTGATGTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: TCCC-AATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|29668996|gb|CB665271.1|CB665271
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|29669368|gb|CB665643.1|CB665643
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTTCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|29676184|gb|CB672459.1|CB672459
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|88376847|gb|CI639172.1|CI639172
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|29625677|gb|CB630688.1|CB630688
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|157650726|gb|EX450360.1|EX450360
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|396941381|gb|HO188590.1|HO188590
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
EST: gi|34475487|gb|CF452785.1|CF452785
EST:     CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG                         CTGTCTACTTGATCCGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT
genomic: CCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCT

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: 61 (upstream exon), 40 (downstream exon)
Score: 2

GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctg ... gttcctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCTTGGTCCGGAAACTCGTGCACGTGCTCAAGCGAGCATCTCTGATTGTCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTGgtaattcctggatgctaatatctgtttagaaatagcatttccaaagtaaccgttcaataatgatgtgaactgtttgttcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG