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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggaattttgcgattaacatattgtctcatcgtcatcatttaatcatttgttattttcgccacacttagctttcgtccagcaatgcagacaagtaacatttcaccaaactgatcttttttcctctgcccattgtgcttgctctctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGCGGGATTTGCTCGCGATCCTTTCGCTCCCACTGAGGCGGAGATCTCCGCC

Basic information

species Oryza sativa
transcript LOC_Os07g48410.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48410.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G311665_T01 (Zea mays), 3'ss of exon 5
gtggaattttgcgattaacatattgtctcatcgtcatcatttaatcatttgttattttcgccacacttagctttcgtccagcaatgcagacaagtaacatttcaccaaactgatcttttttcctctgcccattgtgcttgctctctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGCGGGATTTGCTCGCGATCCTTTCGCTCCCACTGAGGCGGAGATCTCCGCC
||||||||    | | | |||      | |||| ||||||||      |||   |    | | |  || ||| ||||||||||  ||||  ||| ||||| ||||||| |||||  |           |||| | |   |  |||  || ||| |  ||||| || ||||||||||||||||| ||||||||||| | ||||||||  || |||||||| ||||||||  |||  ||   ||||||  | |||
gtggaattagcggctaagcatgcgtcgttatcgccatcatttg-----ttgc-gtccgtgtcgcgttttgctgtcgtccagcagcgcagcgaagcaacatctcaccaa-ctgattct-----------ccatgggg---ggactccatg-cagCGCCGAGCACAACCTGCCGGACAGCCCGTTCGCGTCGCCGACGAGGTCCGCGGCCTTGGCTCGCGACCCTTTCGCGGCCATCGACCGGGAGATGGCTGCC
















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|86253323|gb|CI058248.1|CI058248
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|58603862|gb|CK014390.1|CK014390
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGA
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGA
EST: gi|58657427|gb|CK046107.1|CK046107
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|58676590|gb|CK065277.1|CK065277
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCA
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCA
EST: gi|58607975|gb|CK036008.1|CK036008
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|29666734|gb|CB663009.1|CB663009
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGAACAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|88325268|gb|CI675062.1|CI675062
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|88851800|gb|CI675002.1|CI675002
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|86257029|gb|CI061792.1|CI061792
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|58659889|gb|CK048569.1|CK048569
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|88221815|gb|CI221771.1|CI221771
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|58612737|gb|CK040449.1|CK040449
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|88268546|gb|CI378481.1|CI378481
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
EST: gi|29681057|gb|CB677332.1|CB677332
EST:     GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAG                         TGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC
genomic: GAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGC

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), 74 (downstream exon)
Score: 17

GAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCAACGGAGCCGATAAGGAGGAATCCACCGGAGAGTCCTCCAGCCCTAACACAGACAGTGACCAAAGgtggaatttt ... tctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGCGGGATTTGCTCGCGATCCTTTCGCTCCCACTGAGGCGGAGATCTCCGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcaccaaactgatcttttttcctctgcccattgtgcttgctctctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGCGGGATTTGCTCGCGATCCTTTCGCTCCCACTGAGGCGGAGATCTCCGCC
         aactgat  putative branch site (score: 17)
               tcttttttcctctgcc  CT-rich tract
              atctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggaattttgcgattaacatattgtctcatcgtcatcatttaatcatttgttattttcgccacacttagctttcgtccagcaatgcagacaagtaacatttcaccaaactgatcttttttcctctgcccattgtgcttgctctctttggcagTGTGGAGCATAATCTGCCGGACAGCCCGTTTGCGTCGCCGACCAAGTCCGCGGGATTTGCTCGCGATCCTTTCGCTCCCACTGAGGCGGAGATCTCCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC