Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatataccttgaatttgttctgtcatgacttgcacagtccctccaatgcacaaaattgtgggtacttattttcctacaatttgattttttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCCTAGACGAGCACCCAGAGCTCAGGACTGAGGGAACTCCAACACTGACGCC

Basic information

species Oryza sativa
transcript LOC_Os10g34360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g34360.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G380650_T01 (Zea mays), 3'ss of exon 1
tatatataccttgaatttgttctgtcatgacttgcacagtccctccaatgcacaaaattgtgggtacttattttcctacaatttgattttttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCCTAGACGAGCACCCAGAGCTCAGGACTGAGGGAACTCCAACACTGACGCC---------------
 ||||| | | |  | |  || ||| |||| | |     | ||||| ||  ||| |    || ||| |      |  |  |||| |||||       |||||| ||| || ||||||| ||||||||||||||| ||||| ||||||||  | ||  ||||||||||||| | ||  ||||| ||||| |||||||| ||               
catatacagccttcagtatttatgtgatgattcgatt--tgcctccgataaacaga----tgagtatt---gcccaaatgatttaattttc------caggcacgactacaacagTGAAGACAAGGTACACTGTTATGTCCAAGGAGCTATTGGATAAGCACCCAGAGCTGAAGATGGAGGGTACTCCGACACTGACACCCCGCCTTGACATCTG

upper sequence: LOC_Os10g34360.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G380650_T02 (Zea mays), 3'ss of exon 1
---------------tatatataccttgaatttgttctgtcatgacttgcacagtccctccaatgcacaaaattgtgggtacttattttcctacaatttgattttttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCCTAGACGAGCACCCAGAGCTCAGGACTGAGGGAACTCCAACACTGACGCC
                ||||| | | |  | |  || ||| |||| | |     | ||||| ||  ||| |    || ||| |      |  |  |||| |||||       |||||| ||| || ||||||| ||||||||||||||| ||||| ||||||||  | ||  ||||||||||||| | ||  ||||| ||||| |||||||| ||
agtacaatagatcaccatatacagccttcagtatttatgtgatgattcgatt--tgcctccgataaacaga----tgagtatt---gcccaaatgatttaattttc------cagGCACGACTACAACAGTGAAGACAAGGTACACTGTTATGTCCAAGGAGCTATTGGATAAGCACCCAGAGCTGAAGATGGAGGGTACTCCGACACTGACACC

upper sequence: LOC_Os10g34360.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G477683_T01 (Zea mays), 3'ss of exon 1
tatatataccttgaatttgt-tctgtcatgacttgcacagtccctccaatgcacaaaattg-------tgggtacttattttcctacaatttgattttttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCCTAGACGAGCACCCAGAGCTCAGGACTGAGGGAACTCCAACACTGACGCC
      ||   | |||| || | | || | || |  |   ||  |   |||     | |||       |  | |  |   |   | | |  |||||||  |||  |||||| |||||||||||||||||||||||||||||| ||||| |||||||| || ||  ||||||||||||| | ||  ||||| ||||||||| |||| ||
-----gtatgctaaattggtctttatctttaccttgagtatctatgtgatgatttgatttgcctctagtaagcagatgagtattttccaaatgattttactttc-cagGCACGACCACCACAGTGAGGACAAGGTACACTGTTATGTCCAAGGAGCTTCTGGATAAGCACCCAGAGCTGAAGATGGAGGGTACTCCAACATTGACACC

upper sequence: LOC_Os10g34360.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G13900.1 (Glycine max), 3'ss of exon 1
------tatatataccttgaatttgttctgtcatgacttgcacagtccctccaatgcacaaaattgtgggtacttattttcctacaatttgattttttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCCTAGACGAGCACCCAGAGCTCAGGACTGAGGGAACTCCAACACTGACGCC
      ||   | |   ||    |  | ||        |  | |    |   | |   | ||| ||     ||||  || |      ||   |||   |||  ||||||||| |||||| |||| |||||||||||| || |||||||||||| |||| ||| || |||||||  |    || |||||  | |||||  | | || 
aactactaacaaaaatatgtgcataatttgaatcactatatataaaaacattactaatctaaactgccaacactttcttcc------ttcattttccatttgtcagGCAAGAACACCACTGTGAAGACAAGGTACACAGTGATGTCAAAGGAGATCCTTGACAAGTACCCAGAATTGGCCACAGAGGGCTCACCAACCATAAGGCA

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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgcacaaaattgtgggtacttattttcctacaatttgattttttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCCTAGACGAGCACCCAGAGCTCAGGACTGAGGGAACTCCAACACTGACGCC
                                   atttgat  putative branch site (score: 5)
                                    tttgatttttttttt  CT-rich tract
                      ttattttcctacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatataccttgaatttgttctgtcatgacttgcacagtccctccaatgcacaaaattgtgggtacttattttcctacaatttgattttttttttacagGCAAGACCACCACAGTGAGGACAAGGTACACTGTCATGTCAAAGGAGCTCCTAGACGAGCACCCAGAGCTCAGGACTGAGGGAACTCCAACACTGACGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - -cttgaat
- - - - - - - - - - - tgtcatg
- - - - - - - - - - - - - - -acttgca
- - - - - - - - - - - - - - - - - - - - ccctcca
- - - - - - - - - - - - - - - - - - - - - - - - -gcacaaa