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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctgaaagagaaataagaagtatcaaaagatttgatgatatttttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC

Basic information

species Oryza sativa
transcript LOC_Os07g33954.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G009223_T01 (Zea mays), 3'ss of exon 3
attctgaaagagaaataagaagtatcaaaagatttgatgatatttttgtg-tgat-aatccag---ctgattcatgtggccat------ggatttctctgtggttttgt--------agGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
                    || ||| |      |   |||||||  ||| | || |||||||     | ||| |||||| |       || || |||||||  | ||         |||||||||||||||||||| |||||||||||| |||||||||| ||||||||||||||  ||||||||||||| || || || |||  |||||||||||||
-------------------cagaatcgattaccgtttcgatatttccgtgataatcaatccagagctgggttcgtgtggctaaattaaaggcttcctctgtgcgtgtgcgtgggcgcagGTGGGTGGCGGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCCTACATGTCCCTGGACGAGATCTCGCCCCTCACCTTCTCCATCGGCAACACC

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 3
-----attctgaaagagaaataagaagtatcaaaagatttgatgatatttttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
     | |||          |      |    ||  |       |   || ||| |     |  |     ||  |      ||||||||   ||    |||  |||||||| || || |||||||| ||||||||||||||||| ||||| || ||||||||  | ||  |||| || ||  | ||||||||||| || ||||| 
aattcagtctttttttcttttccttcttccttaaccacccacccaaccttatgtctccctttataaaatgtt-gttaactaatggattttgatg----tttacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCACTTGTACAATCAAGTCTCATACATGTCTCTTGATCAGATTTCTCCCTTAACATTCAGCATTGGAAACACA

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G38830.1 (Glycine max), 3'ss of exon 3
-----attctgaaagagaaataagaagtatcaaaagatttgatgatatttttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
      ||||         ||     |       | |    || |  ||| |   | | |||       ||| || |  | |  | ||| |      ||||  |||||||| || || |||||||| ||||||||||||||||| |||                                                         
aaattgttctcctgttttgattgcctgccaagttaaaaccaatcacttttcttcatca-aatgtttaaaattaat-taactactggttttta---atttttacagGTGGGTAGCTGCCCAGAGTGTCTTCTACCACTTGTACAATCAA---------------------------------------------------------

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 3
-------------------------------------------attctgaaagagaaataagaagtat-caaaagatttgatgatatttttgtgtgataatccagctgattc----------atgtggccatggatttctctgtggt-tttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
                                            |||   ||||    | |    | | |     |||| ||| | ||         |||   ||  |||||          |||| |  |   | |    | || | ||||||||||||| || || |||||||| || |||||||||||||| ||||| || ||||||||  | ||  |||| || ||  | ||||| ||||| || ||||| 
gtaagcacatttttttaattttttactgttagtttttgaattggttcaacaagatttcttattgttgtgctttttatttcatgttgttgggccaaattaacttagtggattctgtttatcaaatgttgttaactaatggattttgatgtttgtagGTGGGTAGCTGCACAGAGTGTCTTTTACCACTTGTACAATCAAGTCTCATACATGTCTCTTGATCAGATTTCTCCCTTAACATTTAGCATTGGAAACACA

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 3
attctgaaagagaaataagaagtatcaaaagatttga-tgat-atttttgtgtgataatccagctgattcatgtggccatggatttctctgtggt----tttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
        | |    ||||||   |  |    ||| | |||| |      ||     ||||   | | | ||  |       |||| ||| |  |    |||| ||||||||||  ||||||||||||||||| ||| | |||||||||||||| |||||||| || ||| | ||||| ||  |||| || ||  | || ||||||
------ctaaacgtttaagaatccttgagtctttttagtgattagggcaatgaatccatcccattcacttatccgattccacatttttctttaatcaaatttgcagGTGGGTGGTTGCGCAGAGTGTGTTCTATCACCTCTACAACCAAGTGTCTTACATGTCTTTAGACCAAATCTCTCCCTTGACGTTTAGTGTTGGTAACACC

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv10s0116g00760.t01 (Vitis vinifera), 3'ss of exon 3
-attctgaaagagaaataagaagtatcaaaagatttgatgatatttttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
  || | ||  |   |   | | |     |   || ||   |    || | ||||     |      | | ||     ||| ||    | ||  | ||||||||||||||||| |||||||| ||||| |||||||| || || || || ||||||||  ||||  ||||||| ||  |||| || ||||| || ||||| 
agttttcaataaactagtggcactgctctatttttagaattttgacttctttgatgccttactaacgtgaagtatgtgtgg-ttctaatttgtatgtgtagGTGGGTGGCGGCTCAGAGTGTCTTCTATCACTTGTATAATCAGGTATCATACATGTCCCTGGATCAGATCTCTCCCTTGACGTTTAGCATAGGAAACACG

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 3
attctgaaagagaaataagaagtatcaaaagatttgatgatatttttgtgtgataatccagctgattca-tgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
||||     |      |   |||   ||  | |  | || | | ||| ||      |   ||| |   | |||     ||| | |   |      | |||||||||||||||| |||||||| ||||| ||| | ||||| || ||||| ||||||||  |||| |||||||| ||  |||| || ||||| || ||||||
attccctgtgtttcccactcagttgtaagtggta-gttgttttctttttgcttggcttttgctaaggaaatgtttgtgtggctgttatttgtacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATACATGTCGCTGGATGAGATCTCTCCCTTGACGTTTAGCATTGGAAACACC

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 3
attctgaaagagaaataagaagtat-caaaagatttgatgatatttttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
|   | | | |||  |   | || | |   |||| ||     ||| ||| | |   |||| ||||||   | |      |        ||| | | || |||||||| | ||| ||||||||||| || ||||||||||| |||||||| |||||||||||| ||||||| || || || ||||| |||||||| || |||
aagatcagatagatgtttcatgttttctgtagatatgtcagcattgttgcgagggcatcctgctgatgt-tttacttgagctgacgattgttgatatgcagGTGGGTCGTGGCACAGAGTGTGTTTTATCACTTGTACAATCAAGTGTCTTACATGTCATTGAACGAGATTTCTCCTCTCACATTTAGCATCGGTAATACC

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S143_174V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------------------attctgaaagagaaataagaagtatcaaaagatttgatgatatttttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
                                                                                       | |  || ||| | |   | ||  | |||  ||    ||   | ||  ||         |||   |  |    |   |       |  | | || |||||||||| ||||||||||||||| ||||||||||||||||| ||||| |||||||| ||| ||||||| || ||||| || |||||||| || ||||||
gtagtcgaatcttcttcctagtctatgccccagaacgtgtaccacgtagttgatgtttcgagtgtggccttgtgcatgagctctcaccagggagggaagtgacctg-atgtacagacatgcgagtagcatggttagagtggaggattgagggagattttgaccaacccacacggtgatgtgcagGTGGGTGGTGGCGCAGAGTGTGTTTTACCACTTGTACAACCAGGTGTCGTACATGTCGTTGCACGAGATTTCGCCACTAACGTTCAGCATTGGTAACACC

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S70_177V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------attctgaaagagaaataagaagt--atcaaaagatttgatgatatttttgtgtgataatccagctgattcatgtggccatggatttctctg----tggttttgt--agGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
                                                                                              | |   | ||| |     ||  |  | |  ||  | |||   |  || |   |    ||   |  ||| ||    |   ||   | ||    ||||| |||  |||||||||| |||||||||||| |||||||||||||||||||| ||||| ||||||||  || ||||||| || |||||||| |||||||| |||||||||
gtagctgcatctattagttttcctgttactactagaacgtaaactgtattgttggtgcggtttttagtatgtgagcttgtgcatgagctttccccaggtggtgaagttttcggtcgagtagagaatgcgttgaggataatgag-agtggagcatgagggtcaggttttaaccaatccgtttggtgatggttgtgtgtagGTGGGTGGTGGCGCAGAGTGTATTCTACCACTTGTACAACCAGGTGTCATACATGTCGCTGAACGAGATTTCGCCACTGACCTTCAGCATTGGCAACACC

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S18_317V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------attctgaaagagaaataagaagtatcaaaagatttgatgat--atttttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
                                                           || | || |     |   |       | ||  ||||   | | ||  |  || |      | |  || || |  | | |  |   ||||    || |||||||| | ||| |||||||||||||||||||| |||||||||||||| ||||||||||||||| | ||||| ||||| ||||||||| | |||||||| 
gtgaagcccccctccaggaacaccttgcagaacacctttgtgtctttacttctgagggttgcaggatatcgcggtgttgctgcgggtttacatgagcgaatattacg-aatgacggtatttaagcaagttgataagaaaatggttgtg-cgatgcagGTGGGTAGTGGCACAGAGTGTGTTCTACCACTTATACAACCAAGTGTCATACATGTCATTGGACAAAATCTCCCCACTCACATTCAGCGTTGGCAACACG

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------------------------------------attctgaaagagaaataa---gaagtatcaaaagatttgatga-tatttttgtgt--gataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
                                                                                       |   |  |||  || | |   || ||  ||    ||  ||||| |||  |||     ||  ||  ||  | ||| |  |      |||   | ||  | | || |||||||||| ||||||||||||||| ||||| ||||||||||| || || ||||||||  || |||||||||||||||| || ||||||||||| ||||||
gtacttgcatattcctctcagcatttataccgagacttgtaccaagtagttgatgtttctgacgtgaccttgtgtttatgagctttcaccttacaagtcaagtgacctgatgtg-cagtgaatgcgatgagtatgattggaatggaggattgagggggttcgtaagt-----gatccgtatggtgatgtgcagGTGGGTGGTGGCGCAGAGTGTGTTTTACCATTTGTACAACCAGGTCTCGTACATGTCCCTGAACGAGATCTCACCACTAACGTTCAGCATCGGTAACACC

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ35859 (Selaginella moellendorffii), 3'ss of exon 3
attctgaaagagaaataagaagtatcaaaagatttgatgatatttttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
           | ||        |     | | ||||   | |   |      |  | |   |  ||  |   ||| |   | |       | |    |||||||||   || ||||| || ||||||||||||||||||||||| || || |||||  ||||| |||| || || ||||| |||||||| || ||||||
-----------gtaacgttggtcacttccaaacttgagactctgccttccccgtcgttc--tttctttctcacgccgtccgtct-------gctaaccagGTGGGTGATCGCACAGAGCGTCTTCTACCACTTGTACAACCAAGTCTCGTATATGTCGCTGGACCAGATATCTCCGCTGACTTTCAGCATTGGTAACACC

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|163928182|gb|EG713578.1|EG713578
EST:     GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTG                         GTGGGTGGCGGCG
genomic: GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTGgtgagcctca ... ggttttgtagGTGGGTGGCGGCG
EST: gi|58587774|gb|CF986082.1|CF986082
EST:     GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTG                         GTGGGTGTGCGGCGCAGAGTGTTGTTCTACCACTTGTACAACCAAGTGTCC
genomic: GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTGgtgagcctca ... ggttttgtagGTGGGTG-GCGGCGCAGAGTGT-GTTCTACCACTTGTACAACCAAGTGTCC
EST: gi|58687050|gb|CK075737.1|CK075737
EST:     GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTG                         GTGGGTGGCGGCGCAGAGTGTGTTCTAC
genomic: GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTGgtgagcctca ... ggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTAC
EST: gi|218501784|gb|FG956611.1|FG956611
EST:     GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTG                         GTGGGTGGCGGCGCAGAGTGTGTT
genomic: GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTGgtgagcctca ... ggttttgtagGTGGGTGGCGGCGCAGAGTGTGTT
EST: gi|58677768|gb|CK066455.1|CK066455
EST:     GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTG                         GTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTA
genomic: GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTGgtgagcctca ... ggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTA
EST: gi|27554106|gb|CA998006.1|CA998006
EST:     GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTG                         GTGGGTGGCGGCGCANAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTA
genomic: GCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTGgtgagcctca ... ggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTA

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), 68 (downstream exon)
Score: 64

TGGTCATCCTCCTCCCTTTCGCCTTCGCCATGGAGGGGCCCAAGGTGTGGGCTGCCGGCTGGCAAAAAGCCGTCGCCGAGATCGGTCCAAACTTCGTCTGgtgagcctca ... ggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC
              agctgat  putative branch site (score: 64)
     tgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attctgaaagagaaataagaagtatcaaaagatttgatgatatttttgtgtgataatccagctgattcatgtggccatggatttctctgtggttttgtagGTGGGTGGCGGCGCAGAGTGTGTTCTACCACTTGTACAACCAAGTGTCCTACATGTCATTGGACGAGATCTCACCACTGACATTCAGCATCGGCAACACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC