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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccttttttttttgttgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA

Basic information

species Oryza sativa
transcript LOC_Os10g38950.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 2
ttccttttttttttgttggg-cggtcaagagcgtgtgatacatttttgactcacacatttatatcatata----gtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
     | |   | |||| |  |  ||||    ||   |    |  |   |    |  ||  ||| || ||    |||| ||  ||||||||||    | ||||||||  ||||| |||||||  ||||||| |||||||  ||||| ||||||||||| || ||||||||| ||||||| |||||||| ||||||||||||||| 
-----tatgcatgtgttagaaccatcaaccatgttgtacttctactcagcaatgaagttcctatgatctaatttgtctaataatgattttaacttgtggtcacagATCCTTGCCTTAAAGGATGTAATTCGGCCCCCAACTAGAGAGAACTTTAATGACGTGTACATTGTTACTGAGTTAATGGATACAGATCTCCATCAGATCG

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 2
-ttccttttttttttgttgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
 || | |     ||| ||    ||     |   |   || |||| ||      ||  || | |  |    |     |    | || |   ||  |   ||| | || ||| | || ||||| ||||| || |||  |||  | ||||| ||||| || |||||||||| |||||| |||||||||||||| ||||| || |
gtttcatgggagtttttttattggattttaattttacattcattattagaattcaatttgaaacaaggctgctcacttaccaatt-acttctctaatgcagGTGATAGCCCTTAAAGACATTATTCGACCACCACAAAGGTATAACTTCAATGACGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAA

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G07270.1 (Glycine max), 3'ss of exon 2
-----ttccttttttttttgttgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
      |  |  |  || | ||  ||  || | |   | || ||    ||| |||  || | |     |  |  |  || |  | | || |   ||  |   ||||||||  |||| || || || || || || |||   |  || ||||| |||||||| ||| ||||||||||||| ||||| || ||||| ||||| || |
attggattttcctcattgtattttgct-tctaaaatctttgtta-gcatttaacttgcaaagtgg--actgactgcttgcttatcaatt-atttctccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAATGATGTGTACCTTGTTTCTGAGTTAATGGACACAGATCTGCATCAAATAA

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G43100.1 (Glycine max), 3'ss of exon 2
ttccttttttttttgttgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
     | |   ||||        |    ||  |   |  |  ||   | |   |  ||| |||      ||||  |  | | |  ||   |   |  ||||| |||||||| | ||| || || || || || ||||  ||   ||| ||||||||||||||||||| ||| |||||||| |||||||| |||||||| |
--gtatctaactttgacttctctttttcagattaataagctcttcctatttctaattttctat------gtctagtaatcaatg-aatcttcttttgcagATAATTGCCATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTCAATGATGTTTACATTGTTTATGAATTGATGGACACTGATCTTCATCAGATTA

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G37480.1 (Glycine max), 3'ss of exon 2
-------ttccttttttttttgttgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
           || | |||| ||       || ||||| |||  | |||||   | |   || ||| | |   |     | |   || | | | |  |    |||||||||||||||| ||||| || || || ||||| | ||  || | ||| |||||||| |||||||||| ||| |||||||| |||||||| || || || |
ttgatctcctattgtcttttcgtctacatttctagagcttgttctccatttacaatt---acctttctgtttaaatacttaaaattgctatcatcttt----cacagATTATTGCCATCAAGGATATCATACGACCCCCCAAAAAGGAAACCTTCAATGATGTGTACATTGTTTATGAATTGATGGACACTGATCTTCACCATATAA

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G02420.1 (Glycine max), 3'ss of exon 2
ttccttttttttttgttgggcggtcaagagcgtgtgatacatttt-tgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
                   |     ||    |  |  | | |||| ||| | |    ||  |||       |||  |  | | |  ||   |   |  ||||| ||||| || | ||| || || || || || ||||  ||   |||| |||||||||||||||||| |||||||||||| |||||||| |||||||| |
-------------------gtatctaactttgaattctcctttttctgattaagctcttcctatttctatttctagtaatcaatg-aatcttcttttgcagATAATTGCTATTAGGGATATCATACGACCTCCCAGAAAGGATGCCTTTGATGATGTTTACATTGTTTATGAGTTGATGGACACTGATCTTCATCAGATTA

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G02060.1 (Glycine max), 3'ss of exon 2
-ttccttttttt--tttgttgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
  |||| || |   |||||       ||   ||| |||  | |||||   | |   || ||| | |  | |    |  |    |||   |   |   ||||||||||||||||| ||||| || || || ||||| | ||  || | ||| |||||||| |||||||||| ||| |||||||| |||||||| ||||| || |
tctcctattgtccgtttgtctacatttctgaagcttgttctccatttacaatt---acctttttgtttttttaattacttaaaattgctatcatctttcacagATTATTGCCATCAAGGATATCATACGACCCCCCAAAAAGGAGACCTTCAATGATGTGTACATTGTTTATGAATTGATGGACACTGATCTTCATCATATAA

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 2
ttccttttttttttgttgggcgg-tcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA-
|| | |      ||  ||   || |    |   |   || |||| ||      ||  || | |  |    |     |    | || |   ||  |   ||| | || ||| | || ||||| || || || |||   || || ||||| |||||||| |||||||||| |||||| |||||||||||||| ||||| || | 
tttcatgggagcttcctgattggattttaattctacaat-cattattagaattcaatttgaaacaaggctgctcacttaccaatt-acttctctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 2
ttccttttttttttgt-tgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagt---ctgatgg--tgatt-ttaacactggatc----acagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
        |||  ||| | |    |||| |  |    | | || || |  | |  ||||||| |   | |||   ||||  |  || || | || | |  |||     ||||||||  |||| || || || || || || |||   |  || ||||| |||||||| ||| ||||||||||||| ||||| || ||||| ||||| || |
-------gtttgatgtgtagattatcaataatgcacaa-atatcttcg--tta-gcatttatcttgcaaagtggactgactgcttggttatcaataatttatccaatgcagATTATGTCCATTAAAGATATTATACGTCCTCCACAGAAGGAAAACTTCAATGATGTGTACCTTGTTTCTGAGTTAATGGACACAGATCTGCATCAAATAA

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G11330.1 (Arabidopsis thaliana), 3'ss of exon 2
ttccttttttttttgttgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
                          |     |||  |  ||||| |    | ||  ||| |   | ||| || ||| || | || ||  ||    |||| || |||  ||||| || || ||| | || ||||  |  ||  | ||   ||||||||| || |||| |||||| |||||||||||||| |||||||| |
------------------------gtaagttttgtactctattttcgcggtaaacgattagagtttctag-ctaatg-tggtcttgac-ttg---tacagGTTGTTGTTATAAAAGATATCATTAGACCACCAAAGAAGGAAGATTTCGTTGATGTTTATATAGTTTTTGAGTTAATGGATACTGATCTTCATCAGATTA

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 2
ttccttttttttttgttgggcggtcaagagcgtgtgatacatttttgac-tcacacatttatatcatat-agtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
                           |  ||||| |   ||  |   | || |   ||| | |  | | | ||| ||  || |||    | ||     ||| | |||||  ||||||| |||||    || ||    ||||| ||||| ||||||||||||||||||| |||| | ||||| ||||||||||| || || |
---------------------------gtacgtgttactaatcatcagcatctctggttttttttgtgtgaatcttatattggttt----attg---tgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAATGATGTTTACATTGTTTATGAGCTTATGGACACTGATCTCCACCAAATTA

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|40491869|gb|BX901732.1|BX901732
EST:     AGCGGACACTGAGAGAAATCAAGCTGCTTCGCCACATGGACCACGAGAAT                         ATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
genomic: AGCGGACACTGAGAGAAATCAAGCTGCTTCGCCACATGGACCACGAGAATgtaagagctg ... tggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
EST: gi|218479396|gb|FG953008.1|FG953008
EST:     CATGGACCACGAGAAT                         ATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
genomic: CATGGACCACGAGAATgtaagagctg ... tggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
EST: gi|66923796|gb|CX110644.1|CX110644
EST:     CTGCTTCGCCACATGGACCACGAGAAT                         ATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
genomic: CTGCTTCGCCACATGGACCACGAGAATgtaagagctg ... tggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
EST: gi|29614215|gb|CB619228.1|CB619228
EST:     AGCGGACACTGAGAGAAATCAAGCTGCTTCGCCACATGGACCACGAGAAT                         ATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
genomic: AGCGGACACTGAGAGAAATCAAGCTGCTTCGCCACATGGACCACGAGAATgtaagagctg ... tggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
EST: gi|58601767|gb|CK012295.1|CK012295
EST:     AGCGGACACTGAGAGAAATCAAGCTGCTTCGCCACATGGACCACGAGAAT                         ATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
genomic: AGCGGACACTGAGAGAAATCAAGCTGCTTCGCCACATGGACCACGAGAATgtaagagctg ... tggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
EST: gi|29614256|gb|CB619269.1|CB619269
EST:     AGCGGACACTGAGAGAAATCAAGCTGCTTCGCCACATGGACCACGAGAAT                         ATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
genomic: AGCGGACACTGAGAGAAATCAAGCTGCTTCGCCACATGGACCACGAGAATgtaagagctg ... tggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
EST: gi|33381800|gb|CF197143.1|CF197143
EST:     GCTGCTTCGCCACATGGACCACGAGAAT                         ATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT
genomic: GCTGCTTCGCCACATGGACCACGAGAATgtaagagctg ... tggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAAT

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: 73 (upstream exon), 40 (downstream exon)
Score: 20

AGTTGCCATCAAGAAGATTGGCAATGCATTCGACAACCATATCGATGCCAAGCGGACACTGAGAGAAATCAAGCTGCTTCGCCACATGGACCACGAGAATgtaagagctg ... tggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA
                                    ttttaac  putative branch site (score: 20)
        acatttatatcatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccttttttttttgttgggcggtcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - -tttgttg
- - - - - - - - - - - - - - -gcgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgg