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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctgtccctgcctacaagacttgctgtttttgctagcatgttacattgctggacggttttgccatgccatgtgagttacgcaattaatcattcttgtctgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA

Basic information

species Oryza sativa
transcript LOC_Os01g05420.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05420.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G085254_T02 (Zea mays), 3'ss of exon 9
--gttctgtccctgcctacaa--gacttgctgtt-------tttgctagcatgttacattgctggacggttttgccatgcc--atgtgagt-----tacgcaattaatcattcttgtctgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA
   | |  |||   | || ||  || | | | ||       |||  ||||  | |   || ||     | ||  | |  |   | ||  |      |  |||||   |  |||||||  |  ||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||| || ||||| || ||||| ||||| |||||||||||| |||| |
gtttaccttccacacttaaaacagattggtttttgccttcctttaatagctagctgagtttcttccgtgcttgcctactcttgaagtaggaccaaatgagcaatagcttgttcttgttggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAGGCGTCGAAGCTCAGCGTGGAAGGCCGTGGCATGATCAAGTACCTGTAGA

upper sequence: LOC_Os01g05420.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G085254_T03 (Zea mays), 3'ss of exon 8
--gttctgtccctgcctacaa--gacttgctgtt-------tttgctagcatgttacattgctggacggttttgccatgcc--atgtgagt-----tacgcaattaatcattcttgtctgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA
   | |  |||   | || ||  || | | | ||       |||  ||||  | |   || ||     | ||  | |  |   | ||  |      |  |||||   |  |||||||  |  ||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||| || ||||| || ||||| ||||| |||||||||||| ||||  
gtttaccttccacacttaaaacagattggtttttgccttcctttaatagctagctgagtttcttccgtgcttgcctactcttgaagtaggaccaaatgagcaatagcttgttcttgttggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAGGCGTCGAAGCTCAGCGTGGAAGGCCGTGGCATGATCAAGTACCTGTAG-

upper sequence: LOC_Os01g05420.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G100881_T02 (Zea mays), 3'ss of exon 9
----------------------------gttctgtccctgcctacaagacttgctgtttttgctagcatgttacattgctggacggttttgccatgccatgtgagttacgcaattaatcattcttgtctgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA
                            | | |||| |     | ||| || |||    || ||  |||| |    || ||   | |   |     |||  ||||  |   |  | ||  |||| ||  | |||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| ||||| || ||||| ||||| |||||||||||| |||| |
gttttccttccatccttaaaacatcttggctttgtctcccttcataag-ctagctagggttcctt-catgct----tgttgactgttgaagtaggaccaactgagcaat--agctgattcttctcgttggacatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAGGCGTCAAAGCTCAGCGTGGAAGGCCGTGGCATGATCAAGTACCTGTAGA

upper sequence: LOC_Os01g05420.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA09G34220.1 (Glycine max), 3'ss of exon 10
gttctgtccctgcctacaagacttgctgtttttgctagcatgttacattgctggacggttttgccatgccatgtga-gttacgcaatt-aatcattcttgtctgtca--tgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA
              |   ||||||  ||  | || ||  || |||  |  || |  ||| |     |     | || || |  |||||  | |  | |   |||||   |||||||||| ||||||||||||||  |||  |||||||| |||||  | ||||||||  ||||| | || || ||||| ||||| |||||||| || || ||||
------------aatctcagactttatgaatgtg-taaaat-ttatgtaccttggtggtatctttgttagtagagatgtgaaccaatttgacctgtgtgaactgtccactgcagATGAATAAGAAATTGCAGCAATTGAGGGCACCAAAAAAGAAGCAGCTTCAGGCTACAAAATTGAGCGTGGAAGGTCGTGGTATGATCAAATATTTATAAA

upper sequence: LOC_Os01g05420.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA01G01610.2 (Glycine max), 3'ss of exon 10
gttctgtccctgcctacaagacttgctgtttttgctagcatgttacattgctggacggttttgccatgccatgtgagttacgcaattaatcattcttgtctgtca--tgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA
              |  | || ||  | |||||  ||  |  |||  |  || |     ||||  |    ||    || ||  | || | | || |   |||||   |||||||||| ||||||||||||||  |||  |||||||| |||||  | ||||||||  ||||||| || || ||||| ||||| |||||||| || || ||||
---------gaattttaatgatttttttttttttata-taaattatgtaccttgttatctttgtta--gtatagatgtgaccaatttgacctttgtgaactgtccactgcagATGAATAAGAAATTGCAGCAATTGAGGGCACCAAAAAAGAAGCAGCTTCAGGCTACAAAACTGAGCGTGGAAGGTCGTGGTATGATCAAATATTTATAAA

upper sequence: LOC_Os01g05420.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G32130.1 (Arabidopsis thaliana), 3'ss of exon 10
gttctgtccctgcctacaagacttgctgtttttgctagcatgttac-----attgctggacggttttgccatgccatgtgagttacgcaattaatcattcttgtctgtca-tgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA
              |   ||||   || ||| ||  || || | |      |    | |  | | || |  | |  |   |||     |  |  |  || |    | | | ||||||||||||||||| | |||||||| |||| | ||||||||||    || || ||  | ||| | || |||||||| || || |||||||||||| | || |
-------------atctgagac---ctttttgtgacagtatataaacaaaaaccctttgttgctctttcttttctctaatagtccttgagctggttcttttgtgttataactgcagATGAACAAGAAACTTCAGCAGCTAAAAGGAACAAAGAAGAAGCGGCTACAAGCTACGAAAGTGAGCGTTGAAGGTCGGGGTATGATCAAGTACCTCTAGA

upper sequence: LOC_Os01g05420.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv07s0104g00230.t01 (Vitis vinifera), 3'ss of exon 10
gttctgtccctgcctacaagacttgctgtttttgctagcatgttacattgctggacggttttgccatgccatgtgagttacgca-attaatcattcttgtctgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA
   || |  || |  ||| |   ||      |||    | ||||   ||  ||     |||| |   | ||    ||||  | | | |  | | |   |  | |  ||||||||||||||||  |||| ||| |||| ||||| || |||||  | ||||| ||  |||||||||| |||||||| ||||| ||| |||| ||||||||  
---ctattgcttc--acatgctgtgtataacttggagacttgttt--ttattgtgtcctttttcttagaca----agttctgaatactgtttaattgcgattttattgcagATGAACAAGAAGCTGCAACAGTTGAAGGCACCCAAAAAGAAGCAGCTTCAAGCTACAAAACTCAGCGTTGAAGGTCGTGGTATGGTCAAATACTTGTAGT

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|33813166|gb|CF332476.1|CF332476
EST:     GCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: GCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|29662253|gb|CB658528.1|CB658528
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGTTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|29670427|gb|CB666702.1|CB666702
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|29679612|gb|CB675887.1|CB675887
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|88220373|gb|CI219933.1|CI219933
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|218504271|gb|FG960657.1|FG960657
EST:     CAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCCAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|88413157|gb|CI523718.1|CI523718
EST:     TGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: TGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|218479478|gb|FG952626.1|FG952626
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|88382235|gb|CI533439.1|CI533439
EST:     GCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: GCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|29665319|gb|CB661594.1|CB661594
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|27577848|gb|CB000543.1|CB000543
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG

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: 68 (upstream exon), 73 (downstream exon)
Score: 31

ATCACCCTTGGACTTTGTTATTCGCCCGCAGTCCAAAATTGATCCCGAACAAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggttttgccatgccatgtgagttacgcaattaatcattcttgtctgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA
                            aattaat  putative branch site (score: 31)
                                     ttcttgtct  putative PPT
                            aattaatcattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctgtccctgcctacaagacttgctgtttttgctagcatgttacattgctggacggttttgccatgccatgtgagttacgcaattaatcattcttgtctgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG