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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgtcccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC

Basic information

species Oryza sativa
transcript LOC_Os10g37520.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 6
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgtcccagtaacattaat-catacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC
                                  | |    |||||  |   |  | |      | | ||  |  |  | |   |||||     | ||   ||  | | || ||||| |||  ||||||||||||||||||| || ||||||||||| ||||||||  | ||||||||| ||||||||||| |||||||||||||  | |||| |||||||||||| |
----------------------------gaaacatgtggataaatagaagttcctctaaatctggtatatatattaggacatctcattttaattattattgttctttcttataaatgttgtcgtgcagGTGAATGCATTCCCAATAACTGTCATGTTCGGCATGTGCTCCATTTTCCTTCTCATGGCAGCAGTCTTGCAGAGGCGCTTAATGGCTGTCTCTGATCTTC

upper sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgtcccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC
                      | | ||      | ||  |    ||  ||    |  |    | | ||||||  |  |     | | | ||    |   | ||||  |  |  |  |    |||||||  |||||||||| |||||||| ||||||||||||||  | |||||||||||  ||||    |||||||| ||||| ||||||||  | || |||   |
---------------------gtatgttacacaatctactacttcaatgcaatg-cttgagcttaccaatgcagtagtatttt-cttatctctggttttgactaattgtgtattttct-cgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC

upper sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 6
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgtcccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC
                   |  |      | | ||   | || | ||  | | | |     | || |   | |       | | | | ||          | ||||  |  |  |  | |  |||||||  |||||||||| |||||||| ||||||||||||||  | |||||||||||  ||||    |||||||| ||||| ||||||||  | || |||   |
----------------gtatgttacacaatctactacttcaatacaatgcgcgatcttaacagtgtagtagtattttcttatg-cgtgtgctttg-----actaattgtgtattttct-tggtgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCGGATAAGC

upper sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgtcccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC
         ||| |||  |     || |||||                 |||||   || |  ||  | | |       |      | |||    ||   | | |  |     ||| || |||| |||| ||||||||||| ||||| ||||||||||| |||||  | || ||||| ||  | |||    || | || |||||||| ||| |  |   |||    |
--------gtaagtccccccaacattctttttct--------------gcacca--tagtagctgagatttcgtgtcccatgtctctgtgtt---gtggtactgactagttttatg-tgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC

upper sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgtcccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC
         |  |      |  || ||| || |||| |  | |   | | |   |        |||   | |   || |  | | ||| ||          ||  || | |        || || |||| |||||||| || |||||||||||||||||||||||  | |||||||| ||  ||||| || | ||||| ||| |||| ||| |  | || ||   ||
---------tgtactgttttaatggtttcttctcttaaccatagggata-atttatctctctctgctcct-ctctaacactaaatattggt----------ttgttcttcc------ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC

upper sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgt-cccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC
                            || || |  ||  | |  |       ||    |  |||   | |       |  |    || |      ||| | |  |  |    ||| |  | || |||| |||||||||||||||||||||||||||||||||||  | |||||||| ||  ||||| | |||||||| |||||||| |||||  |  ||||     
--------------------------ccttattttggatatagaccatgtgaagacttctatgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtt--tttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT

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|88839829|gb|CI017594.1|CI017594
EST:     ACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAAT                         GTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
genomic: ACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAATgtaagtagct ... tgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
EST: gi|86594290|gb|CI251162.1|CI251162
EST:     ACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAAT                         GTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
genomic: ACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAATgtaagtagct ... tgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
EST: gi|58668185|gb|CK056871.1|CK056871
EST:     CTTCTTCCGCATACCACTCAACCTGTTTGGTTTGTGTGGTTCTTTACAAT                         GTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
genomic: CTTCTTCCGCATACCACTCAACCTGTTTG-TTTGTGTGGTTCTTTACAATgtaagtagct ... tgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
EST: gi|58657621|gb|CK046301.1|CK046301
EST:     GTGGTTCTTTACAAT                         GTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
genomic: GTGGTTCTTTACAATgtaagtagct ... tgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
EST: gi|88907822|gb|CI091220.1|CI091220
EST:     ACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAAT                         GTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
genomic: ACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAATgtaagtagct ... tgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
EST: gi|86502603|gb|CI145236.1|CI145236
EST:     ACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAAT                         GTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
genomic: ACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAATgtaagtagct ... tgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
EST: gi|7134671|gb|AU082614.1|AU082614
EST:     ACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAAT                         GTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
genomic: ACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAATgtaagtagct ... tgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
EST: gi|86492295|gb|CI134928.1|CI134928
EST:     ACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAAT                         GTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT
genomic: ACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAATgtaagtagct ... tgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTT

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: 73 (upstream exon), 70 (downstream exon)
Score: 18

GAAGATGAGGTCCCAGTATATTCCTGAGGAGGCAAGAAGCACGATCATGAACTTCTTCCGCATACCACTCAACCTGTTTGTTTGTGTGGTTCTTTACAATgtaagtagct ... tgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaaaagacatttgtcccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC
                            attaatcatacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgtcccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT