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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatactcaacctatttaatgtatctttgtttttctaccttttattttgttttacatttatgtccctacctgattgcatgtattctgtttcccgtgtcatcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG

Basic information

species Oryza sativa
transcript LOC_Os05g38610.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G883149_T03 (Zea mays), 3'ss of exon 3
gttatactcaacctatttaatgtatctttgtttttctaccttttattttgttttacatttatgtccctac-ctgattgcatgt-attctgtttcccgtgtcatcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG
|||||  ||   ||||| || || | | | ||   | |   ||| || ||||  |  ||  |||    |  ||||||| || | | | |||||||    |    |||||||| || |  || |||||||| ||||||||||| ||| |||| || ||||||||||| || ||||||||||||||||||||
gttatcttccctctattgaa-gtttatcttttcaaccattgtttgttctgttacatgttattgtgttaatgctgattgtatatgaatgtgtttccaaccttggtggtttcagGAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGACCTGATCCTATTGTGTCTTGATGAAATTGTTGATGGAGG

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G431350_T01 (Zea mays), 3'ss of exon 3
gttatactcaacctatttaa-tgtatctttgtttttctaccttttattttgttttacatttatgtccctac-ctgattgcatgt-attctgtttcccgtgtcatcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG
|||||  ||   ||||| || | ||||||||     |    |||| || ||||  |  ||  |||    |  ||||||| || | | | |||||||  | |    ||||||||||| |  || |||||||| ||||||||||| ||| ||||| | |||||||||||||| ||||||||||||||||||||
gttattttccctctattaaactttatctttgcaac-cactgttttgttctgttacatgttgttgtgttaatgctgattgtatatgaatgtgtttccaatcttggtggtttcagAAACATGGTTGACAAAAGGACAGCACTCGAGAATTTGGATATGATCCTATTGTGCCTTGATGAAATTGTTGATGGAGG

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G02270.3 (Glycine max), 3'ss of exon 3
gttatactca-acctatttaatgtatctttgtttttctaccttttattttgttttacatttatgtccct--acctgattgcatgtattctgtttcccgtgtcatcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG
||| |  ||  || ||   ||| ||| | ||||   | |  ||  |   ||||||  || |||  |  |  ||    | |    |  |   ||| | || |  ||   |  |||   || || ||||| |    |||||| || ||  |||||||||| ||||||||| | ||||||||||||||||| ||
gttgtggtcttacataaacaatttatatatgtt---ccatgttcaagggtgtttttaatctatcactattaacacagtagtccttgatgattttactgtcttttcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATAGATGAAATTGTTGATGGCGG

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G13190.2 (Glycine max), 3'ss of exon 3
gttatactcaacctatttaatgtatctttgtttttctaccttttattttgttttacatttatgtccct--acctgattgcatgtattctgtttcccgtgtcatcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG----------------------
||| || ||    |||| |   | | | | | ||||    ||  |   ||||||  || |||  |  |  ||    | |    |  |   ||| | |  |  ||   | ||||   || || ||||| |    |||||| || ||  |||||||||| ||||||||| | ||||||||||||||||| ||                      
gttgtaatct-tatattaacaatttatctatgtttc-gtgttcaagggtgttttcaatctatcactattaacacagtagtccttgatgattttactgccttttcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATTGATGAAATTGTTGATGGCGGGTATGCTATATGCTATTCATAT

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G13190.3 (Glycine max), 3'ss of exon 3
gttatactcaacctatttaatgtatctttgtttttctaccttttattttgttttacatttatgtccct--acctgattgcatgtattctgtttcccgtgtcatcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG
||| || ||    |||| |   | | | | | ||||    ||  |   ||||||  || |||  |  |  ||    | |    |  |   ||| | |  |  ||   | ||||   || || ||||| |    |||||| || ||  |||||||||| ||||||||| | ||||||||||||||||| ||
gttgtaatct-tatattaacaatttatctatgtttc-gtgttcaagggtgttttcaatctatcactattaacacagtagtccttgatgattttactgccttttcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATTGATGAAATTGTTGATGGCGG

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G02270.2 (Glycine max), 3'ss of exon 3
gttatactca-acctatttaatgtatctttgtttttctaccttttattttgttttacatttatgtccct--acctgattgcatgtattctgtttcccgtgtcatcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG----------------------
||| |  ||  || ||   ||| ||| | ||||   | |  ||  |   ||||||  || |||  |  |  ||    | |    |  |   ||| | || |  ||   |  |||   || || ||||| |    |||||| || ||  |||||||||| ||||||||| | ||||||||||||||||| ||                      
gttgtggtcttacataaacaatttatatatgtt---ccatgttcaagggtgtttttaatctatcactattaacacagtagtccttgatgattttactgtcttttcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATTGTGCATAGATGAAATTGTTGATGGCGGGTATGCTATATGCTATTCATAT

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|58696220|gb|CK084907.1|CK084907
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|88983146|gb|CI020710.1|CI020710
EST:     TAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTGTCAGG                         AGATTACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTAT
genomic: TAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCA-Ggttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTAT
EST: gi|33688934|gb|CF317173.1|CF317173
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33692847|gb|CF321086.1|CF321086
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|396941400|gb|HO188609.1|HO188609
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33692848|gb|CF321087.1|CF321087
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|8857691|gb|AU095009.1|AU095009
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|29682909|gb|CB679184.1|CB679184
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33820855|gb|CF336232.1|CF336232
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33820857|gb|CF336233.1|CF336233
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGAACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTAT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCG-ACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTAT
EST: gi|163918457|gb|EG713211.1|EG713211
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33678548|gb|CF306787.1|CF306787
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|218504818|gb|FG952248.1|FG952248
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|218500698|gb|FG952590.1|FG952590
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|58585721|gb|CF984029.1|CF984029
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33683273|gb|CF311512.1|CF311512
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT

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: 71 (upstream exon), 62 (downstream exon)
Score: 38

AAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttatgtccctacctgattgcatgtattctgtttcccgtgtcatcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG
             acctgat  putative branch site (score: 38)
                       atgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatactcaacctatttaatgtatctttgtttttctaccttttattttgttttacatttatgtccctacctgattgcatgtattctgtttcccgtgtcatcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG