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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctatagagattgctcttcttttggttattattctgttattatttagtaggcagcatgacgagcggtattacattgttgtatggtgcag

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 29
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 6
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgta-------atctatagagattgctcttcttttggttattattctgttattatttag-taggcagcatgacgagcggtattacattgttgtatggtgcag
 ||||| |||||||| |||||  ||||||||||||  || || ||||||||||||| ||| || ||||||||||| || ||||||||||| ||||||||||||       ||||  |   |    |  | |||  || ||||  |  ||  |  | ||  ||   ||||||| |||    || | || ||| |        
ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAAATCGAGTCACAGAATGAAGAAAGAGCCAAAGAGAAGGAGGAGAAAGATCTTGTGGCTCAGCAGgtacatctaaatcttcactcacatgttctgtttgtgtaattaaccatttcatgctgaggcagttggcatgacaagctacgttccgtt-ttgcag-------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 6
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgta-------atctatagagattgctcttcttttggttattattc-tgttattatttagtaggcagcatgacgagcggtattacattgttgtatggtgcag
 ||||| |||||||| |||||  ||||||||||||| ||||| ||||||||||||| ||| |  ||||||||||| || ||||||||||||||||||||||||       ||||  |   |    |  | ||   || |||| || | | ||  |   | ||   ||||||| ||     || |||| ||| |        
ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAGAATTGAGTCACAGAATGAAGAAAGAGTCAAAGAGAAGGAGGAGAAAGATCTTGTTGCTCAGCAGgtacatctaaatcttcattcacatgttctgttcgtgtaattaatcatttcatcctgaggcagttggcatgacaagttacgttccatt-ttgcag-------

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 9
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctatagagattgctcttcttttggttattattctgttattatttagtaggcagcatgacgagcggtattacattgttgtatggtgcag
 ||||| |||||||| |||||  |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||   |||||||||||| |     | |  || ||    |  ||| |  ||| |    |  | ||       |||||| ||  | |||    ||   | ||  |   
ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTGCGACTCAGCAGgtaaacct--aaaaccgcgctcgcgtgtgttttgtttccg----tgctgaggcattgacatgacaagttgcattcttatgcgatgtgcag---

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 14
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctatagagattgctcttcttttggttattattctgttattatttagtaggcagcatgacgagcggtattacattgttgtatggtgcag
 ||||| |||||||| |||||  |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||| ||||||||||||| |     | |  || ||    |  ||| |  ||| |    |  | ||       |||||| ||  | |||    ||   | ||  |   
ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTGTGGCTCAGCAGgtaaacct--aaaaccgcgctcgcgtgtgttttgtttccg----tgctgaggcattgacatgacaagttgcattcttatgcgatgtgcag---

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GRMZM2G115138_T01 (Zea mays), 5'ss of exon 13
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctatagagattgctcttcttttggttattattctgttattatttagtaggcagcatgacgagcggtattacattgttgtatggtgcag
 ||||| |||||||| |||||  |||||||||||| ||| || || ||||| |||| ||| ||||| |||||||| || ||||| ||||  ||||||||||||| |     | |  || ||    |  ||| |  ||| |    |  | ||       |||||| ||  | |||    ||   | ||  |   
ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCTAAGGAGAAGGAGGAGAAAGACCTTGCGGCTCAGCAGgtaaacct--aaaaccgcgctcgcgtgtgttttgtttccg----tgctgaggcattgacatgacaagttgcattcttatgcgatgtgcag---

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GRMZM2G057576_T01 (Zea mays), 5'ss of exon 28
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctatagagattgctcttcttttggttattattctgttattatttagtaggcagcatgacgagcggtattacattgttgtatggtgcag
 ||||| |||||||| |||||  |||||||||||| ||| || || ||||| |||| ||| || || |||||||| || ||||| ||||| ||||||||||||| |     | |  || ||    |  ||| || ||   |   |  | ||       |||||| ||  | |||    ||   | ||  |   
ATACACTAGCAAGGTGGATGATTTAGTGAAGGACAAGATCGAGTCGCAGAAGGAAGAAAGAGCCAAGGAGAAGGAGGAGAAAGACCTTGTGGCTCAGCAGgtaaacct--aaaaccgcgctcgcatgtgtttttgtt---tccgtgctgaggcattgacatgacaagttgcattcttatgcgatgtgcag---

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 29
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatct--------------atagagattgctcttcttt-------tggttattattctgttattatttagtaggcagcatgacgagc-----ggtattacattgttgtatggtgcag----------
||| ||  | || |||||||||||  | |||||||  |||||| ||||||| || |  |  ||||||||||||||||| || ||| || ||||||||||||||  ||              |||   | |||| | | ||         | || ||| || ||  | ||  |||   |   |  | |       | ||| | |||  |    | | ||           
GTATACTGGTAAAGTTGATGAGCTTATCAAGGACAAAATTGAAGCACAGAAAGAGGAGAAAGCTAAAGAGAAGGAAGAGAAGGATGTTATTGCTCAGCAGgtacactccccccctcccccaatatcaaatgctttccattatgaagtcagataatatcctttttcttttgggtacatattttatctaatatttggctatcaaattaatactagtttcaattatctccag

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 29
lower sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 29
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctatagagattgctct-tcttttggttattattctgttattatttagtaggcagcatgacgagcggtattacattgttgtatggtgcag---------------------------------------------------------------------
||||||  |||| || ||||| |||||||||||||  |||||| |||| |||||||| | |||||||||| | |||||||| ||| | ||||| || ||||||||   |  |  |    || ||  |  || |  | | ||   |  | |   | |     ||  ||    |  |    | | | ||  | ||                                                                      
GTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATTGAAGCACAAAATGAAGTGAAGGCTAAAGAGCAAGAAGAAAAGGATGTAGTTGCACAACAGgtaattattttatgtcatgctgtcactctgtcagcagtttga-gtgttctgaaatgtttgttgttgataaatcctcatctttcgcatcattcatcctcgactttctcaacagattgaacattagagtagtactgatatgaatgagatgtgctttttgttgcag

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|87030226|gb|CI270236.1|CI270236
EST:     ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAG                         AACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
genomic: ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctata ... tatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
EST: gi|89180594|gb|CI044873.1|CI044873
EST:     ATCTTGTTGCTCAGCAG                         AACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
genomic: ATCTTGTTGCTCAGCAGgtaatctata ... tatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
EST: gi|27334465|gb|CA882916.1|CA882916
EST:     ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAG                         AACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
genomic: ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctata ... tatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
EST: gi|29685119|gb|CB681394.1|CB681394
EST:     ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAACAG                         AACATGTATGCCCAATTGCTTCCTCTTGCCTTGCCTGCTCCTCCTGGTATG
genomic: ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctata ... tatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
EST: gi|29664582|gb|CB660857.1|CB660857
EST:     ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAG                         AACATGTATGCCCAATTGCTTCCTTTCGCCTTGCCTGCTCCACCTGGTATG
genomic: ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctata ... tatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
EST: gi|29627717|gb|CB632728.1|CB632728
EST:     ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAG                         AACATGTATGCCCAATTGCTTCCTCTTGCCTTGCCTGCTCCTCCTGGTATG
genomic: ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctata ... tatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
EST: gi|29626374|gb|CB631385.1|CB631385
EST:     ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAG                         AACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
genomic: ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctata ... tatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG
EST: gi|29624173|gb|CB629184.1|CB629184
EST:     ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAG                         AACATGTATGCCCAATTGCTTCCTCTTGCCTTGCCTGCTCCTCCTGGTATG
genomic: ATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctata ... tatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATG

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), 66 (downstream exon)
Score: 143

GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctata ... tatggtgcagAACATGTATGCCCAATTGCTTCCTCTCGCCTTGCCTGCTCCACCTGGTATGGGCGGTCCTCCACCGCCAATGGGGATGCCGGGCATGCCTCCGATGGGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTGTTGCTCAGCAGgtaatctatagagattgctcttcttttggttattattctgttattatttagtaggcagcatgacgagcggtattacattgttgtatggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA