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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctaaatgattttgccacatcttataagttttgaataaaggccatgggcagaagtaatctgtgaattttgtttcttattgttatgctatgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACAAGCAAAAGG

Basic information

species Oryza sativa
transcript LOC_Os12g10560.1
intron # 4
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 4
lower sequence: GRMZM2G052713_T01 (Zea mays), 3'ss of exon 4
tttctaaatgattttgccacatcttataagttttgaataaaggccatgggcagaagta--atctgtgaattttgtttcttattgttatgctatgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACAAGCAAAAGG
 | ||   |   | |   |  | ||       || ||  |     | |     || ||  || |||||||||  ||  | ||  ||  ||||| | ||||||||||| ||||||||||||||||| ||||| |||||||| |||||||| ||||||||||||
ctgct--tttgctctttaatcttttgccttccttaaaccatactaaagtatctaactatcatttgtgaatttgcttattgatcttttggctatctgctgtagGTTTACTTGATATTGGATGAGTTCATTCTTGCTGGAGAGCTTCAAGAAACAAGCAAAAGG

upper sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S220_70V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------tttctaaatg-attttgccacatcttataagttttgaataaaggccatgggcagaagtaatctgtgaatttt---gtttcttattgttatgctatgttct-------gtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACAAGCAAAAGG
                                                                         ||  ||| |    |    |    |||   | | |     |   ||  |  |   |    |||   ||||   || | | |   | |  | || |||          |||| |||||||||||||||||||| ||||| ||||| ||| | ||||| || ||||||| |
gtacacgcgcgtcgtttcttctggcatttgacgcatgtgcagtctatatattcgataacaatgcatcgtgcacctggatgtacccggatgtaggcaatagaatct-atcgtggattatatgacgctttttagtgtttgttttcaagtgtgtaagaatgacaccattttcatctactgacagGTGTATTTGATATTGGATGAGTTCATTCTTGCTGGTGAATTGCAAGAAACCAGCAAAAAG
















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:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|88244598|gb|CI243720.1|CI243720
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|88244271|gb|CI243393.1|CI243393
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|8404493|gb|AU091847.1|AU091847
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|88238097|gb|CI237946.1|CI237946
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|88987133|gb|CI034174.1|CI034174
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|33689088|gb|CF317327.1|CF317327
EST:     TTTCTTCAGCAATGTGTGTGAACTCGACTTANGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: TTTCTTCAGCAATGTGTGTGAACTCGACTTA-GTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|88995546|gb|CI022869.1|CI022869
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|33669785|gb|CF298024.1|CF298024
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|87015947|gb|CI279699.1|CI279699
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|58683184|gb|CK071871.1|CK071871
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|33693746|gb|CF321985.1|CF321985
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|33659105|gb|CF281718.1|CF281718
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|33689089|gb|CF317328.1|CF317328
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|33693747|gb|CF321986.1|CF321986
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|66923463|gb|CX110311.1|CX110311
EST:     ATTTCTTCAGCAATGTGTGGGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAG
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAG
EST: gi|38478254|gb|CF962387.1|CF962387
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|86878703|gb|CI340589.1|CI340589
EST:     CAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: CAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|33663155|gb|CF294122.1|CF294122
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
EST: gi|88238521|gb|CI238370.1|CI238370
EST:     ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAG                         GTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA
genomic: ATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACA

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: 59 (upstream exon), 60 (downstream exon)
Score: 27

TGAGTTGGCATACTTGGAATGCATCCACTTGTTTGTCGAGATATTAGATCATTTCTTCAGCAATGTGTGTGAACTCGACTTAGTATTTAATTTCCACAAGgtaacagcta ... tgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACAAGCAAAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgggcagaagtaatctgtgaattttgtttcttattgttatgctatgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACAAGCAAAAGG
                    aattttgtttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctaaatgattttgccacatcttataagttttgaataaaggccatgggcagaagtaatctgtgaattttgtttcttattgttatgctatgttctgtagGTTTATTTGATATTGGATGAGTTTATTCTCGCTGGAGAACTTCAAGAGACAAGCAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - -ttgccac
- - - - - - - - - - - - - - - - - gaataaa
- - - - - - - - - - - - - - - - - - - - - - catgggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgct