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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtgctactaacttgtcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcatgaagtctctaacttgttgcatttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC

Basic information

species Oryza sativa
transcript LOC_Os09g10600.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G079256_T01 (Zea mays), 3'ss of exon 2
----aagtgctactaacttgtcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcatgaagtctctaacttgttgcatttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
    | |  ||   || || |  |  ||   |||  || |  |    |||||     ||  |     | |  | |    || |   | |||||  ||||  ||||||||||||||||||| ||||||||||||||||||||||| ||||| |||||||| || || ||||||||||| |||||||| |||||||||||||||||
gtacatgatctggcaattttttttatctatgggatctgaactaat--gcacatattcaataactgcaagttttcagacatcaattatcttgcaagtttt--cagGTAAAAGAGCATTTATAGCTGGAGTTGCTGATGATAATGGTTATGGTTGGGCAATTGCTAAGGCTCTTGCTGCTGCTGGTGCTGAGATTCTTGTTGGTAC

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 1
aagtgctactaacttgtcattactgaaggaaatgtataatctagc-acaacccaaaggatatttaatca--tgaagtctctaacttgttgcatttttt-tacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
       |  || |||| ||| |  |  | |   | |    || |             || ||| ||    ||  |  |   |||   || || |  |   |||||||||| || || |||||||| || |||||||| ||||| ||||||||||||||||||||| |||| || ||||| || || || |||||||| || ||
----ctcataaatttgttattgccaagtgtaccttttttcttaactgtccttttttatatctttgatttgttgtggcattccactgaatgtatgtgatgcgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTCGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G03060.1 (Glycine max), 3'ss of exon 3
aagtgctactaacttg--tcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcatgaagtctctaacttgttgcatt--tttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
 | |  |  ||| |||  |  |||       | |  |||    |         || ||  |||  || ||   | |   | |||      |    | | |  ||||||||| || ||||||||||| ||||||||||| ||||| ||||| |||||||| |||||||||||||||||||| || || ||||| |||||||| ||
-aattttg-taatttgattggttatcttttcatagatatggatttttctg--tcatagagtatgaaaacaaatattgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAAGCTCTTGCTGCAGCAGGAGCTGAGATCCTTGTTGGCAC

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 2
aagtgctactaacttgtcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcat-gaagtctctaacttgttgcatttt--tttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
   |   |  || |||| ||| |  |  | ||  | |    ||  ||       |     || | || | |  |  |   |||   ||   | |  | | |||||||||| || || |||||||| || |||||||| ||||| ||||||||||||||||||||| ||||||| ||||| || || || |||||||| || ||
---tctcataaatttgttattgccaagtgtaacttttttcttactaccttttttatatctttgattcgttgtggcattccactgaatgttatgtgatgtgcagGTAAAAGGGCTTTCATTGCTGGTGTGGCTGATGACAATGGATATGGCTGGGCAATAGCAAAATCTCTTGCAGCAGCAGGAGCTGAAATTCTTGTCGGCAC

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 2
--aagtgctactaacttgtcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcatgaagtctctaacttgttgcatt--tttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
     ||  | |   |||    |  |     | || |  | | |   |  |     ||  |||   | ||   |     | |||      |    | | |  ||||||||| || ||||||||||| ||||||||||| ||||| ||||| |||||||| |||||| ||||||||||||| || || || ||||||||||| ||
aattttgtaatttgattggttatcttttcatagatatggattttgctatgat----agagtatgagaacaaatatcgctttactgaaaatagcaatatatgtagGTAAAAGGGCTTTTATTGCTGGTGTTGCTGATGACAATGGATATGGATGGGCAATTGCAAAATCTCTTGCTGCAGCCGGAGCTGAAATTCTTGTTGGCAC

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 2
aagtgctactaacttgtcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcatgaagtctctaacttgttgcatttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
                       ||   |  || | |    | |   ||  || || | | ||  |  |       ||||     || |  |  | ||||| |||||||| || ||||||||  | |||||||||||||||||||| ||||| ||||||||| |||||||||| ||||| || || ||  | ||||| ||
---------------------gttggttggcatatctttctttg---aattcagagaagacttggtgctatctgaactaagcaagtgtaaatggt-acagGGAAAAGAGCTTTCATTGCTGGTATAGCTGATGATAATGGCTATGGTTGGGCCATAGCAAAATCTCTTGCTGCTGCTGGAGCTGAAATATTGGTTGGGAC

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 2
aagtgctactaacttgtcattactgaaggaaatgtataatctag-cacaacccaaaggatatttaatcatgaagtctctaacttgttgcattttttta-cagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
|||  | |  || |  |   | ||        | |   |  | | ||||    |        |  ||  |||     ||||| |  ||  |  |  |  ||||||| || ||||||||||| || || |||||||||||||| ||||| ||||||||||||||| | |||||||| || || || || |||||| |||| ||
aagaacca--aattaattgcttctaccacttgtttgatacttggtcacacaatatgaacccatctattttgactaaactaacatagtgagtaatactggcagGTAAGAGGGCATTTATTGCGGGTGTAGCTGATGATAATGGATATGGTTGGGCAATAGCAAAATCGCTTGCTGCTGCAGGAGCTGAAATTCTTATTGGCAC

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 2
--aagtgctactaactt---gtcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcatgaagtctctaacttgttgcatttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
    ||| |   || ||   |  |||  |||     ||   | ||    |||||   |||  | |||   || | || |    ||  ||       | | |  |||||| ||||| ||||||||||| ||||||||||| ||||| ||||| ||||||||||| ||| ||||||| || || ||||| || ||||||||||| ||
gtttgtgatttcaaatttaagatatttgtgaccttgattattgataagacacaaa--aaataagattacctcttcaacta---aaactgggattgctatctgtagGTAAGAGAGCCTTTATTGCTGGTGTTGCTGATGACAATGGATATGGTTGGGCAATAGCCAAATCTCTTGCAGCTGCAGGTGCTGAAATTCTTGTTGGCAC

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|88396638|gb|CI619971.1|CI619971
EST:     GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAG                         GTAAAAGAGCATTTATTTGCTGGAGTTGCTGATGATAATGGCTA
genomic: GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAGgtaagcttta ... ttttttacagGTAAAAGAGCATTTATT-GCTGGAGTTGCTGATGATAATGGCTA
EST: gi|58660187|gb|CK048867.1|CK048867
EST:     GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAG                         GTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
genomic: GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAGgtaagcttta ... ttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
EST: gi|58658677|gb|CK047357.1|CK047357
EST:     GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAG                         GTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
genomic: GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAGgtaagcttta ... ttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
EST: gi|58683660|gb|CK072347.1|CK072347
EST:     GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAG                         GTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
genomic: GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAGgtaagcttta ... ttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
EST: gi|88400623|gb|CI596044.1|CI596044
EST:     GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAG                         GTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGC
genomic: GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAGgtaagcttta ... ttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGC
EST: gi|29670466|gb|CB666741.1|CB666741
EST:     GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAG                         GTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
genomic: GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAGgtaagcttta ... ttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
EST: gi|58655118|gb|CK043798.1|CK043798
EST:     TTTGCCGTGAGGGCGATGTCTGCCCAGGGGACTCCCCATTGATCTCAGAG                         GTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
genomic: TTTGCCGTGAGGGCGATGTCTGCCCAGGG-ACTCCCCATTGATCTCAGAGgtaagcttta ... ttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
EST: gi|29640101|gb|CB645110.1|CB645110
EST:     GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAG                         GTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
genomic: GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAGgtaagcttta ... ttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
EST: gi|86894525|gb|CI308263.1|CI308263
EST:     GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAG                         GTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG
genomic: GTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAGgtaagcttta ... ttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGG

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: 69 (upstream exon), 47 (downstream exon)
Score: 11

TGCAGAAAAACAGCATCAGCAGGGCCGTTTGTTTCTCTGAACCACAAGAGGTTTGCCGTGAGGGCGATGTCTGCCCAGGGACTCCCCATTGATCTCAGAGgtaagcttta ... ttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaacccaaaggatatttaatcatgaagtctctaacttgttgcatttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC
                             ctctaac  putative branch site (score: 11)
                                          cattttttt  putative PPT
            atatttaatcatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtgctactaacttgtcattactgaaggaaatgtataatctagcacaacccaaaggatatttaatcatgaagtctctaacttgttgcatttttttacagGTAAAAGAGCATTTATTGCTGGAGTTGCTGATGATAATGGCTATGGCTGGGCAATAGCAAAAGCTCTTGCTGCAGCTGGTGCCGAGATTCTTGTTGGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- -tgctact
- - - - - - - - - -ttactga
- - - - - - - - - - - - - - - - - - - - - - - -aacccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttgc