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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG

Basic information

species Oryza sativa
transcript LOC_Os10g33720.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactacacctcattggact-cataaaa---attgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
   |||     |   |  || | ||| |  | |   |  ||      ||  || || |    |     |||   ||   |  || | |   | |   ||| |||||||| |||||||||||||||||||||||| | |||||||||||||| ||||| ||||||||||||||| | ||||||||||||||||| |||||| |||
--ggtttaacacgtccactgaccttccactatatactcatctgaaatta--gttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G107629_T03 (Zea mays), 3'ss of exon 4
--------tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
          ||  | | |  |   |      |     ||| |  ||     ||      |   |||||| ||   |   ||  ||| || |   |||   ||| ||||| || |||||||||||||||||||||||| | || ||||||||||| ||||| ||||||||||||||| | ||||||||||||||||| |||||| |||
taataacacgtgccctgacagactgaccttcctatctgaaattagttctgtttg-----attgcatccttgctgagctgtatccgacccaca---attttttttccagGTCCCTATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
--------tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
          ||  | | |  |   |  |||| |||   |||  |  |   ||   | ||    |||||| ||   |   ||  ||  || |    ||   ||| ||||| ||||||||||||||||||||||||||| | || ||||||||||| ||||| ||||||||||||||| | ||||||||||||||||| |||||| |||
taataacacgtgccctgacagactga--ccttccaatctaaaattagttctgtttgattgc---atccttgctgagctgtatccgatccaca---tttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
--tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
       |  |   |   |||   |       || |     ||   | |  ||||  |||  ||| | || |   |     |  ||     | |  |||||||| || || || |||||| ||||  | |||   || |||||||||||||| || || |||||||||||||| ||||| || ||||||||||||||| |||
gtgaaaatttgctaagagtatatgtgatcttcaacacaccctctgatacatatgtattatt-ttagtccaacatttgttgtttcta-----taatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
--------tctgttccgtccaatctatgcctttcaaaa--aaaatgttttca--agtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
        | ||    | | |   |  |   || || |  || || |  ||   | | |   |||   ||  | |  |      | |    ||        ||   |||||||| || || || |||||| | ||  | |||   |||||||||||||||||||| ||||| |||||||||||||||||||| |||||||| ||||||||||
gtaaagaatatgccgagactaga-tgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgttcatcagtgtctaataatttctgtttctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatcct-tactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
                 |    || | || |  || | |   |     ||| | || ||   ||||  |  | ||||   |  |  | ||  |  ||||||||||| || || |||||| ||||  | |||   ||||||||||||||||| || || |||||||||||||| |||||||| |||||||||||||||| ||
--------------gtgaaaatttgctaagagtatatgt--gatcttcaatatactctctgatactg-atgtaattg---ttgtttatat-aatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
--------tctgttccgtccaatctatgcctttcaaaa--aaaatgttttca--agtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
        | ||    | |     | ||   |||||    || || |  |||  | | |   |||   ||  |  | |  |   |                ||   || ||| | || || || |||||| | ||  | |||   |||||||||| ||||||||| ||||||||||||||||| |||||||| |||||||| ||||||||||
gtaaagaatatgccgagactcga-tgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatcc--ttactac-acctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
                  || || ||     | ||||| |  |||  ||  |   |      |||| |  || | | ||   ||      | | |  ||  ||||||| || ||||||||||||||  | |||   ||||||||||  || || || || ||||| ||||||||||||||||| ||||| || |||||| |||
-----------------gtgtctatcg----atatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaat-atgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 3
tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactac-acctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
  || |   |    | | |   |||      |  |||  |    | ||  |  | |   |||  ||     |  ||    |  ||   |||  | ||  ||||||| || || ||||| || ||| | |||   |||||||||||||| || || ||||||||||||||| | |||||||| || ||||| |||||| |||
-gtgctatatttgctttcttgttttgctttgatttgtgattggttcctggttacattgtcttgatattgttttgttc--tttgtattgatttgcgtt-tagGTTCCTATTAAGTGGCCTAAGAGTAGAGATGAAGTGTGGAAAGCAAACATACCTCACACTCACCTTGCAAAAGAGAAGTCTGATCAGAACTGGATGGTTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactaca-cctcattggactcataaaaat---tgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
                              | |||||    |||    |  ||   |    |  |  |   |  ||    |  |     |   |  | |||||| | || || || |||||||||||  | |||   || ||||||||||| || || || |||||||||||||||||||| || ||||||||||||||| |||
---------------------------gtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 3'ss of exon 2
tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactacacctcattggactcataaaaattgacttt--------------gcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
     |  |||    ||     |||   ||| | ||    ||||      | |  | |  | | ||  || ||| | ||  |  |  |||  |||                ||||| || || || ||||| |||||  | |||   ||||||||||| ||||| || || || |||||||||  ||||||||| |||||||| |||||| |||
----gtgagtctgtgcttaagttttttgaaatattgggaccaaggaagtttatattgttttcattat-ccacat-gtacctaagatgattctcttctgctgtgggcggtaacagGTCCCAATCAAGTGGCCTAAAAGCAGAGATGAGGTGTGGAAAGCCAATATACCTCATACCCACCTTGCAACTGAGAAGTCTGACCAGAACTGGATGGTTG

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|33675210|gb|CF303449.1|CF303449
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|27554159|gb|CA998059.1|CA998059
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|44676356|gb|CR289790.1|CR289790
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|163926509|gb|EG712373.1|EG712373
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|33676827|gb|CF305066.1|CF305066
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|33676729|gb|CF304968.1|CF304968
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
EST: gi|33797110|gb|CF324420.1|CF324420
EST:     CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAG                         GTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT
genomic: CTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATT

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), 55 (downstream exon)
Score: 6

GATGAAACTGGATTTAAACCTGATGGAACACTACGAGAGGCATTGCCCTCCTCCTGAAAGGCGCTTGAACTGCCTGATTCCCCCACCACATGGCTATAAGgtcccaagat ... gactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
                                    ataaaaattgacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT