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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattatttgtcattctccctaagcggctaagccacctatcagttgccggtaagaaaaaaagttcataccgtcataacatgagatgctattgctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACGCAGACAACTCCGAAGGAGAGAAGAAGACTAAAATTGGTTCTTTCAAGAA

Basic information

species Oryza sativa
transcript LOC_Os05g46720.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G355610_T01 (Zea mays), 3'ss of exon 2
tattatttgtcattctccctaagcggctaagccacctatcagttgccg-gtaagaaaaaaagttcatacc----gtcataacatgagatgct---attgctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACGCAGACAACTCCGAAGGAGAGAAGAAGACTAAAATTGGTTCTTTCAAGAA
      ||    |     |||| |  |  |      || | | |||   | || ||||| || || |  |     |  | | |||  |  ||   |  ||   ||||||||||||||| |||   ||||| ||||||| |||||||| ||||||||| ||||||||||| |||||||| ||||||||||| || || |||||||||||
------tttctgtctagtctaacccacctaagag--taactgctgctacggaacaaaaatagctctttgcttggattttgagatggaaaactgagacagcctttgcagGTTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATGCAGACAACTCAGAAGGAGATAAGAAGACTAAGATCGGATCTTTCAAGAA

upper sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G174990_T02 (Zea mays), 3'ss of exon 2
tattatttgtcattctccctaagcggctaagccacc--tatcagttgccg-gtaagaaaaaaagttcataccgtcataacatgagatgcta--ttg------ctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACGCAGACAACTCCGAAGGAGAGAAGAAGACTAAAATTGGTTCTTTCAAGAA
           ||     |||| |  |  | | |    || | | |||   | || |||| || ||  |    |   |  | ||||||  |  |||          |||||| |||||||| |||   ||||| ||||||| |||||||| ||||||||| ||||||||||| |||||||| ||||||||||| ||||| |||||||||||
-----------atctagtctaacccacctacctaatagtaactgctgctacggaacaaaataactttctttgcttggattaggagatgggaaattgagacaatctttgcagGCTTTGAAGGGTTTGTACATAACGATGAAAGGAAAGAGAGCAGATCTGATGCAGACAACTCAGAAGGAGATAAGAAGACTAAGATTGGGTCTTTCAAGAA
















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|88417178|gb|CI576252.1|CI576252
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88423499|gb|CI579211.1|CI579211
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29628429|gb|CB633440.1|CB633440
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88299560|gb|CI574673.1|CI574673
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88716785|gb|CI740295.1|CI740295
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29631056|gb|CB636065.1|CB636065
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29636608|gb|CB641617.1|CB641617
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29635051|gb|CB640060.1|CB640060
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29623352|gb|CB628363.1|CB628363
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29624625|gb|CB629636.1|CB629636
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88401724|gb|CI591051.1|CI591051
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88404383|gb|CI578260.1|CI578260
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88386210|gb|CI572827.1|CI572827
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29630847|gb|CB635856.1|CB635856
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29628211|gb|CB633222.1|CB633222
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|25798393|gb|CA754354.1|CA754354
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88399898|gb|CI585817.1|CI585817
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88403007|gb|CI568781.1|CI568781
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88386060|gb|CI570695.1|CI570695
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|33657793|gb|CF280407.1|CF280407
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29628534|gb|CB633545.1|CB633545
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCACGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|58595020|gb|CF993328.1|CF993328
EST:     GAGGTCGGAGGAGGGGATGTCAGGACCACTAGATCGATTTG-CAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GA-ATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88409627|gb|CI568917.1|CI568917
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|33675068|gb|CF303307.1|CF303307
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29669409|gb|CB665684.1|CB665684
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88331717|gb|CI640748.1|CI640748
EST:     GGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29640888|gb|CB645895.1|CB645895
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|29636223|gb|CB641232.1|CB641232
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
EST: gi|88417438|gb|CI579099.1|CI579099
EST:     GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCAT                         GTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG
genomic: GGAATCGGAGGAGGGGATGTCAGGACCACTCGATCGATTTGCCAGGCCATgtgagtacga ... gctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccggtaagaaaaaaagttcataccgtcataacatgagatgctattgctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACGCAGACAACTCCGAAGGAGAGAAGAAGACTAAAATTGGTTCTTTCAAGAA
                         tcataac  putative branch site (score: 2)
        aaaaaaagttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattatttgtcattctccctaagcggctaagccacctatcagttgccggtaagaaaaaaagttcataccgtcataacatgagatgctattgctggtgcagGTTTTGAAGGTTTTACGCATAATGATGAAAAGAAAGAGATCAGATCTGACGCAGACAACTCCGAAGGAGAGAAGAAGACTAAAATTGGTTCTTTCAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - ttctccc
- - - - - - - - - - -agcggct
- - - - - - - - - - - - - - - - - - - - -gttgccg
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cataccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agatgct