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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatacaggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 24
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 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 9
--------------------------------------------------------------------------gtatatatacaggagca-acctg--ttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacac-------ccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
                                                                           || |  ||   | ||| || ||  ||    |||     | ||| | | |||   || | | || ||  || ||||| |||        | |||||||| |||||||||||  | || ||||| ||||| |||||||||||||||||||| |||| |||||||||| | |||||||| |||||||| ||||| || ||||| |
gtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatat-ttctttctgacatagctgctctttttttgtttagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
gtatatatacaggagca---acctgttagaactaa--aacatatttcagtacaagtcttttcttatctagattttttctaacaccctt----------ttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
||||| |   |||||||   || || ||    |    |   | ||| |  |||   ||| | | |||||  || | ||| |||    |          |||||| ||||||||||| ||||| ||||| ||||| ||||||||||| |||||||| |||| |||||||||| | |||||||| |||||||| ||||| || ||||| |
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctat-ttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
gtatatatacaggagca---acctgttagaa-----ctaaaacatatttcagtacaagtcttttcttatctagattttttctaaca--------cccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
||||| |   |||||     || || |         |||     | ||| | | |||   || | | || ||  || ||||| |||        |  |||||||| |||||||| ||  |||| ||||| ||||| |||||||||||||||||||| |||| |||||||||| | |||||||| |||||||| ||||| || ||||| |
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatat-ttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
gtatatatacaggagca---acctgttagaact----aaaacatatttcagtacaagtcttttcttatctagat-------tttttctaacacccttttttgtat--------agGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
||||| |   |||||||   || || ||    |    |  |  |  || |   ||   ||| | | |    |||       ||||||| | | |   ||||||||        |||||||||| ||||| ||||| ||||| |||||||| || |||||||| ||||||||||| ||| | |||||||| |||||||| ||||| || ||||| |
gtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
------gtatatata-caggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
        || || | ||   |||||  ||   |  || |   |   | |||       |||   |   | ||||  |  |        || || |  |||| ||||||||||| || || ||||| |  ||||||||||||||||| || |||||||| || || || ||||| ||||| || |||||||||||||| |
attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
--gtatatatacaggagcaacctgttagaactaaaac----atatttcagtacaagtcttt--tcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
  |||   | | |  |  |||  || | |   |||      ||   |  ||  ||   |||   ||| |||  ||  || ||| |    ||| |  |  |||| |||||||||||||| || || || ||||| |||||||||||||| ||||||||||| || || || ||||| |||||  ||||| |||||||||| |
tagtagcaaaatactaaaaacaagtgacagaaaaacttttgattgctttgtctaaccttttgaccttgtctgaatacttactatc-tgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
------gtatatata-caggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
        || || | ||   |||||  ||   |  || |   |   | |||       |||   |   | || |  |  |        || || |  |||| ||||||||||| || || ||||| |  || |||||||||||||| || |||||||| || || || ||||| ||||| || |||||||||||||| |
attgggaaatgtagaacattggcaacaagtgccagatagactgttgattagtttgttattttctgttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 23
-----gtatatatacaggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacaccctttt---ttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
       | | || | |     |    ||  | ||  |   | |||   |   ||||||| |  ||    ||| | || |    | || |   ||   ||||| ||||| ||||| || || |||||||| ||||| || ||||| || |||||||| || || ||||||||||| |||||| ||||| | || || || |
aggagaaaaaaatgctgtgagcattacttgaatctgcagtttgtttaccttatagtctttcca-atgcttattatgtcaattttcattgtgaatttggtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCCCTCATGGAGAGTGGTTTAGGATTAGAACGGGCAC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 24
---gtat--atatacaggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtat---agGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
   |||   | ||||   | |||  ||  ||||  |      ||| |  ||     | |||      |   |   | | |||   || || | |||   |||| |||||||||||||| || || || || || || ||||||||||| ||||||||||| || || || ||||| |||||  ||||| |||||||||| |
ctagtagcaaaatactaaaacaag-tgacagaaaaacttttgattgctttatctaaccttttggcgttgtctgaataccaactatctgttatatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
--------------gta-tatatacaggagcaacctgttagaa---ctaaaacatatttcagtacaagtcttttct-----tatctagatt-ttttctaacacccttttttgt-----atagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
               || |    |||  ||   ||  ||| |     || |    | ||  |||    |  |  |      |||||   || ||| ||        |||| ||     |||||| |||||  |||| ||||| || || ||||||||||||||||| || ||||||||| | || || || ||||| ||||| || || || || |||||||
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
gtatatatacaggagcaacctgtt----agaa-----ctaaaacatatttcagtacaagtcttttcttatctagattttttctaacaccctttt--ttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
||  ||| | |  ||   |  |||    ||||      | |   ||| ||  ||   | | |    ||     |  ||||| ||| |   || |  ||  |||||| |||||  |||| |||||||| || |||||||||||||||||||| ||||||||| | || ||||| ||||| ||||| || || ||||| |||||||
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatatttttgtgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
gtatatatacaggagcaacctgttagaactaaaacatatttcagtac----aagtcttttcttatctagattttttctaacaccc--ttttttgta----tagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
    ||  |       |  |  ||| |||   |  || || |  ||     ||  ||  || | | |  ||  | | | |       | |||| |     ||||| ||||||||||| ||||| ||||| || ||||||||||| ||||| || ||||| || || || |||||||| |||||  | ||| |||| ||||| |
---aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 24
-------------------------------------------------------gtatatatacaggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagatt--ttttctaacacccttttttg-----tatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
                                                       ||   |  | |    |   ||||  || ||   |    |     |     | |||| |||||  |  |  ||| |||      |  ||||     | ||||| |||||||||||||| || ||||| || |||||||| |||||||| |||||||| || || || |||||||| |||||||| ||  |||||||||| |
gtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtagGTCGATGATTTGGAGGAGGTCAGTGATTATTACCAGAATAGAGGATGCTTCAATGAGCTAATATCACTCATGGAGAGTGGTCTGGGCTTGGAGCGTGCAC

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
gtatatatacaggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
                              |    ||| ||     |  ||  |    |||||    ||  |||||     | ||   |  |||| ||||||||||||||||| ||||| ||||||||||| || ||| | ||| ||||||| ||||| || |||||||||||||| ||||| || || || |
---------------------------gtaaggctatagttt----ctggttatactctatctttggttggtctaatctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC

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|29624172|gb|CB629183.1|CB629183
EST:     CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAG                         GTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
genomic: CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatac ... ttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
EST: gi|218479721|gb|FG960857.1|FG960857
EST:     CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAG                         GTTGATGATTTGGAGGAAGTCAGTGAATACTACCAGAACAGAGGATGTTTC
genomic: CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatac ... ttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
EST: gi|88574701|gb|CI666470.1|CI666470
EST:     CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAG                         CTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTCC
genomic: CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatac ... ttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
EST: gi|29624230|gb|CB629241.1|CB629241
EST:     CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAG                         GTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
genomic: CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatac ... ttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
EST: gi|29663093|gb|CB659368.1|CB659368
EST:     CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAG                         GTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
genomic: CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatac ... ttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
EST: gi|112785583|gb|EE590994.1|EE590994
EST:     CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAG                         GTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
genomic: CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatac ... ttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
EST: gi|88333307|gb|CI642344.1|CI642344
EST:     CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAG                         GTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC
genomic: CCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatac ... ttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTC

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: 75 (upstream exon), 72 (downstream exon)
Score: 195

GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatac ... ttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagtacaagtcttttcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC
                                ttctaac  putative branch site (score: 195)
                            ttttttctaacaccct  CT-rich tract
                   ttatctagatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatacaggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA