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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgggagtatcatcaagtttcaaaatgttacttctgacagcagtctttggtatatgggaatcagtatattcactttctttgtgataattttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC

Basic information

species Oryza sativa
transcript LOC_Os12g10560.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G052713_T03 (Zea mays), 3'ss of exon 3
tgttgggagtatcatcaagtttcaaaatgttacttctgacagcagtctttggtata-tgggaatcagtatattcactttctttgtgataattttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC
   |   |   |    ||   | |  ||   |  | | | |  |   |    |  | ||    |    |   |         ||||  | || ||||||||||||| ||||| ||||||||||| ||| ||||||||||||| |||||||| || |||||||| ||||| ||||| || ||||||||||||||||| ||||
-agtaataaacttccaaaaactaaggattagatatttaatatgaccataaatttcactgtttgttctaactcttgtaactgatgtgggatttctcatgcagTTCCGCACGCACAAAGTTATATATAGGAGATATGCAGGACTTTTTTTCTCTATATGTGTGGACATCACCGACAACGAATTGGCATACTTGGAATGTATCC

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 3
----------------------------------------------------------tgttgggagtatcatcaagtttcaaaatgttacttctgacagcagtctttggt-atatgggaatcagtatattcactttctttgtgataat----tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC
                                                            ||     |  ||| ||  ||| |   | | |||||        |||| |||  | |      |  || | |   || |  | ||||| |    | || ||||||| || ||||| ||  | ||||||||||||||||| ||  ||||||||||||| ||||| ||||||||||| ||||||||||| || || || |||||||
gtcagtactctctccacgattttcaatttcttcctttgctttcgctgagttgtaattgcattatttctgacatgaatgttctatgaggttcttcttttgttgctcttaggttgtctcatttgctatacaattgattgccgtttgatagtaacttgtcttgcagTTTCGTACGCACAAGATAATATACAGGCGATATGCTGGGTTGTTTTTCTCAATCTGTGTTGATATCACTGATAATGAGTTGGCGTATTTAGAGTGCATCC

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G37730.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------tgttgggagtatcatcaagtttcaaaatgttacttctgacagcagtctttggtatatgggaatcagtatattcactttctttgtgataattt-tcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC-
                                                           ||     | |||| ||  ||| |   | | || ||        |||| ||| | |   |||   ||||   | |   ||  || ||| || || ||||||| || ||||| ||  | ||||||||||||||||| ||  | ||||||||| | ||||| ||||||||||| ||||||||||| || || || ||||||| 
tcagtgctctctccaccattttctccttcttcctttgctttcacgaagttgtaattgcattaattctgtcatgaatgttctatgaggttctgcttttgttgctcttaggt-tgtctaaattgttataacaattgatttgttggtaacttgtcttgcagtTTCGTACGCACAAGATAATATACAGGCGATATGCTGGGTTATTTTTCTCACTCTGTGTTGATATCACTGATAATGAGTTGGCGTATTTAGAGTGCATCCA

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 3
tgttgg-gagtatcatcaagtttcaaaatgttacttctga-cagcagtctttg-gtatatgggaatcagtat-attcactttctttgtgataattttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC
|||    ||| | ||  ||  |  ||   |||   | |||   |  ||| ||| | || |     |  | || ||  |  |  ||||  |  |||||||    |||  | || || || || ||||||||||| ||||| ||| ||||||||||  |||| |||||||| || |||||||||||||| ||||||||  | ||||
tgtgattgagaaacaataatatggaatgcgttttatgtgagtgggtgtcattgtgaatgttaatgtatgaatgatgaaactgttttgcaactattttca----gTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCTGTGTGCGTGGATATAACCGACAATGAGTTGGCTTACTTGGAGAGTATCC

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0023g03340.t01 (Vitis vinifera), 3'ss of exon 3
-tgttgggagtatcatcaagtttcaaaatgttacttctgacagcagtctttggtatatgggaatc-agtatattcactttctttgtgataattttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC
   ||  ||| |        |||   | | ||  || | | | || | | | | |  ||   ||  || ||  | |  |      |   | ||| | | |||||||| || || || || || |||||||||||||| ||| |||| |||||| ||||||| ||||||||||| |||||||| ||||| ||||| |||||||
agatttagagcagggggtcctttgtgactatt--ttattaaatcattgtgtagcagctgtccattgagcatgattaagtaggagatttaattttcctttcagTTCCGTACACACAAGGTCATCTACAGGCGATATGCTGGATTGTTCTTCTCATTGTGTGTTGATATCACTGATAATGAGTTAGCATATTTGGAGTGCATCC

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 4
-tgttgggagtatcatcaa--gtttcaaaatgttacttctgacagcagtctttggtatatgggaatcagtatattcactttctttgtgataattttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC
        | ||| |||||   ||| | ||  |||| | |    || ||  |   |||  |   |   |   |||     |  || | | | ||||| |||||||||| || || || || || |||||||||||||| ||| | ||||||||| ||||||| ||||| || || |||||||||||||| || || |||||||
ccagcacaattattatcaattattttataacattacctttacatgctgttctc--tattggattaagggctgattatacctgattataa-atttttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC

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|33669786|gb|CF298025.1|CF298025
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|428995|gb|D25151.1|D25151
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|8404493|gb|AU091847.1|AU091847
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACA-GCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|86899168|gb|CI298074.1|CI298074
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|87015947|gb|CI279699.1|CI279699
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATTGCAGGACTGTTTTTCTC
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATA-TGCAGGACTGTTTTTCTC
EST: gi|88414379|gb|CI691539.1|CI691539
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|58683184|gb|CK071871.1|CK071871
EST:     GTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: GTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|33693746|gb|CF321985.1|CF321985
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|33659105|gb|CF281718.1|CF281718
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|33689089|gb|CF317328.1|CF317328
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|33693747|gb|CF321986.1|CF321986
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|66923463|gb|CX110311.1|CX110311
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|88310668|gb|CI672531.1|CI672531
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|88352823|gb|CI678848.1|CI678848
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|4881090|gb|AU065389.1|AU065389
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|38478254|gb|CF962387.1|CF962387
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|88353193|gb|CI654459.1|CI654459
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|33663155|gb|CF294122.1|CF294122
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
EST: gi|88307351|gb|CI641991.1|CI641991
EST:     TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAG                         TTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA
genomic: TGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCA

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: 51 (upstream exon), 70 (downstream exon)
Score: 44

GTGCATCGGCTGGTGGTCAACCGGGATCCCAAGTTCACCAACTTCGTTGAGgtgagttctt ... tttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttggtatatgggaatcagtatattcactttctttgtgataattttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC
                                            ttttcat  CT-rich tract
                                  tttgtgataatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgggagtatcatcaagtttcaaaatgttacttctgacagcagtctttggtatatgggaatcagtatattcactttctttgtgataattttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC

- - - - - - - - - - - - - - - -acttctg
- - - - - - - - - - - - - - - - - - - -cagcagt