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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgaacacttgcatgataaataattcaagggcttgttgtaatggttgttttatgtttttttttctgtcatgtgattctaaatcattctgttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCTTCTAAGGCTGTTAGTTCAGAACAGAATTGCAGAGTTCCACACTGAGCTG

Basic information

species Oryza sativa
transcript LOC_Os07g25420.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g25420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G073077_T01 (Zea mays), 3'ss of exon 3
---gatgaacacttgcatgataaataatt-caagggcttgttgtaatggttgttttatgtttttttttctgtcatgtgattctaaatcattctgttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCTTCTAAGGCTGTTAGTTCAGAACAGAATTGCAGAGTTCCACACTGAGCTG
    |  |  || | || | ||  |  || || | || ||    |||   ||| ||||| |      | |   || |||| | ||||  |  |  |||||| || ||||||||||| || |||||| ||||||| ||||| ||||| || |||||||| |||||||| |||||||| |||||||| |||||||| |||||||||
tcaaaacattacctccagggtattttttttcaggagcatgccagaat---tgtattatgctaaacaatgtaa-atttgataccaaatggtatttatttatgcagTGGCATAATTCCCCCCTCACCAGAGGAGTACCCAATTTTGGGACTCAATCTTCTGAGGCTGTTGGTTCAGAATAGAATTGCTGAGTTCCATACTGAGCTG

upper sequence: LOC_Os07g25420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G367216_T01 (Zea mays), 3'ss of exon 1
--gatgaacacttgcatgataaataattcaagggcttgttgtaatggttgttttatgtttttttttctgtcatgtgattctaaatcattctgttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCTTCTAAGGCTGTTAGTTCAGAACAGAATTGCAGAGTTCCACACTGAGCTG
   || ||   || | |      || ||    ||      |  | | |||| ||||| |     || |   || |||| | || | ||     |||||| || |||||| |||| ||||| ||| ||||||| ||||| ||| | || | |||||| ||| ||||  |||| || |||||||| || |||||||||||||||
agaatcaaacattacctctagggtattttttaggaacac-gccaggattgtattatgctaaacattgtaa-atttgataccaagtgatatatatttatgcagTGGCATAGTTCCCCCATCGCCAGAGGAGTACCCAATTTTGAGACTCAGTCTTCTCAGGTTGTTGATTCATAATAGAATTGCCGAATTCCACACTGAGCTG

upper sequence: LOC_Os07g25420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G121452_T01 (Zea mays), 3'ss of exon 3
---gatgaacacttgca-tgataaataattcaagggcttgttgtaatggttgttttatgtttttttttctgtcatgtgattctaaatcattctgttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCTTCTAAGGCTGTTAGTTCAGAACAGAATTGCAGAGTTCCACACTGAGCTG
       |||| |  |  |  |   |  |||| | || || |  |||   ||| ||||  |      | |   || |||| | |||| ||  |  |||||| || |||||||||||  | || ||| ||||||| ||||| ||||| || |||||||| |||||||| |||||||| |||||||| || |||||||||||||||
ataatcaaacattacctctcgtttttttttcaggagcatgctagaat---tgtattatactaaacgatgtaa-atttgataccaaatgatatttatttatgcagTGGCATAATTCCCGCCTCGCCAGAGGAGTACCCAATTTTGGGACTCAATCTTCTGAGGCTGTTGGTTCAGAATAGAATTGCCGAATTCCACACTGAGCTG

upper sequence: LOC_Os07g25420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S68_29V6.1 (Physcomitrella patens), 3'ss of exon 3
-gatgaacactt-gcatgataaataattcaagggcttgttgtaatggttgttttatgtttttttttctgtcatgtgattc-taaatcattctgttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCTTCTAAGGCTGTTAGTTCAGAACAGAATTGCAGAGTTCCACACTGAGCTG
  || ||  |||    |  || ||| |||    |     || |||     | |  |||||   |||  |||||||  ||    ||||| |   |    || || ||  | ||||| || ||   ||| |||||||| || || ||||| ||  | ||  ||||||||||||||||||||||||| || || || || |     
atataaattctttatgtattacata-ttcgtctgagaactgaaattcacatatc-tgtttgagtttg-gtcatgtttttagctaatcagttcttcgattgcagGGGGGTGATTCCTCCGTCCGGACAAGAGTATCCCATTTTAGGTCTCAACTTGCTGCGGCTGTTAGTTCAGAACAGAATTGCGGAATTTCATACAG-----

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|8856245|gb|AU093563.1|AU093563
EST:     CATTTGAAAGGGACTTTTGTCAACTCAAACCCTTATTACATGGATACATG                         CGGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTNGGTCTTAATC
genomic: CATTTGAAAGGGACTTTTGTCAACTCAAACC-TTATTACATGGATACATGgttagttcct ... ttttatgaagCGG-CATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATC
EST: gi|88412237|gb|CI573513.1|CI573513
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGG
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGG
EST: gi|33658971|gb|CF281584.1|CF281584
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88333830|gb|CI643862.1|CI643862
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAG
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAG
EST: gi|88424460|gb|CI608046.1|CI608046
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88328055|gb|CI649853.1|CI649853
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCCAC-ACAGGAGTATCCAATCTTGGGTCTTAATC
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATC-ACCACAGGAGTATCCAATCTTGGGTCTTAATC
EST: gi|58681161|gb|CK069848.1|CK069848
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88364221|gb|CI612170.1|CI612170
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAAC-TTATTACATGGATACATG                         CGGCATAATTC-ACCATCACCACAGGAGTATC-AATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88345880|gb|CI632353.1|CI632353
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAAT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAAT
EST: gi|88358913|gb|CI619417.1|CI619417
EST:     GCATTTGAAAGGGAATTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|2427780|gb|C72243.1|C72243
EST:     GCATTTGAAAGGG-CTTTTGTCAACTNAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGGGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88395474|gb|CI612996.1|CI612996
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88377414|gb|CI602899.1|CI602899
EST:     CATTTGAAAGTGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGA
genomic: CATTTGAAAG-GGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGA
EST: gi|88391840|gb|CI603359.1|CI603359
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCAGCACAGGAGTATCCAATCTTGG
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGG
EST: gi|88726404|gb|CI750059.1|CI750059
EST:     CATTTGAAAGGGACTTTTGTCAACTCAAACCCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: CATTTGAAAGGGACTTTTGTCAACTCAAACC-TTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|33654136|gb|CF276750.1|CF276750
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88305511|gb|CI630673.1|CI630673
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAAT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAAT
EST: gi|218496609|gb|FG945909.1|FG945909
EST:     GCATTTGAAAGGGACTTCTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCGCAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88393359|gb|CI618247.1|CI618247
EST:     CATTTGAAAGGGACTTTTGTCAACCTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: CATTTGAAAGGGACTTTTGTCAAC-TCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88305623|gb|CI631990.1|CI631990
EST:     GCATCTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTA
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTA
EST: gi|58586987|gb|CF985295.1|CF985295
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88392419|gb|CI612893.1|CI612893
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|218495940|gb|FG948496.1|FG948496
EST:     GCATTTGAAAGGGACTTCTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCGCAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|218498577|gb|FG966054.1|FG966054
EST:     GCATTAGAAAGGGACTTCTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCGCAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
EST: gi|88326392|gb|CI659822.1|CI659822
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACA
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACA
EST: gi|88383951|gb|CI631841.1|CI631841
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCC
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCC
EST: gi|2443022|gb|C74793.1|C74793
EST:     GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATG                         CGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT
genomic: GCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCT

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), 75 (downstream exon)
Score: 131

ACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAGATGCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATACATGgttagttcct ... ttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCTTCTAAGGCTGTTAGTTCAGAACAGAATTGCAGAGTTCCACACTGAGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttatgtttttttttctgtcatgtgattctaaatcattctgttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCTTCTAAGGCTGTTAGTTCAGAACAGAATTGCAGAGTTCCACACTGAGCTG
                              ttctaaa  putative branch site (score: 131)
                                        ttctgtttt  putative PPT
     ttatgtttttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgaacacttgcatgataaataattcaagggcttgttgtaatggttgttttatgtttttttttctgtcatgtgattctaaatcattctgttttatgaagCGGCATAATTCCACCATCACCACAGGAGTATCCAATCTTGGGTCTTAATCTTCTAAGGCTGTTAGTTCAGAACAGAATTGCAGAGTTCCACACTGAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT