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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCCTGAGCAAGTTCTTCCCCAGGAGAAGGTCGTCGAGACCTACCTCCAGGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttgttcatgtcacttggtattttacatcctgctttctaggtttgagaattttcagaagccaacatagttggcttagctctcctgaaaaatata...

Basic information

species Oryza sativa
transcript LOC_Os10g34360.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g34360.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G380650_T01 (Zea mays), 5'ss of exon 1
CTCCCTGAGCAAGTTCTTCCCCAGGAGAAGGTCGTCGAGACCTACCTCCAGGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttgtt----catgtcacttggtatttta------catcctgctttctaggtttgagaattttcagaagccaacatagttggcttagctctcctgaaaaatata
 | ||||| |||||||| || ||||||||||| || |||| ||||||||| || | || |||||||||||| || || ||||| |||||  |  | |||||| || ||  ||    |||  || ||| | || ||      |||| ||  |||  |  |||| ||||||   | | | ||| |    ||||||||||  | | ||     
TTTCCTGACCAAGTTCTGCCTCAGGAGAAGGTTGTGGAGAGCTACCTCCAAGAAAGCAGCTGCGACGATCCCGCCACCAGGGCCAAGCTTCAGCGCCTTTgtaagcttctttgtttcatcacagttgttgttctataaattcatcttgtcttcacg--ttgaaaatttt---aggtcgacaaatgcagcttagctctagtcataa-----
















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|88414383|gb|CI691543.1|CI691543
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88579867|gb|CI691858.1|CI691858
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88588915|gb|CI706762.1|CI706762
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88410631|gb|CI686968.1|CI686968
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88460117|gb|CI695318.1|CI695318
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88587308|gb|CI705044.1|CI705044
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88588691|gb|CI706527.1|CI706527
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88577156|gb|CI673714.1|CI673714
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88337997|gb|CI676980.1|CI676980
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88419633|gb|CI686851.1|CI686851
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88578239|gb|CI687159.1|CI687159
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88582476|gb|CI699890.1|CI699890
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88334729|gb|CI676519.1|CI676519
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|32948059|gb|BP184631.1|BP184631
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
EST: gi|88589758|gb|CI708563.1|CI708563
EST:     GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTT                         GCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC
genomic: GGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttg ... ttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCC

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCCTGAGCAAGTTCTTCCCCAGGAGAAGGTCGTCGAGACCTACCTCCAGGACACCATCTGCGACGATCCTGCAACAAGGGCAAAGCTGGAAAGACTTTgtgagttttgttcatgtcacttggtattttacatcctgctttctaggtttgagaattttcagaagccaacatagttggcttagctctcctgaaaaatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata