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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaatctcagctatcgattcttttcatgatcatcttcctagctagtggtactactccagatcagaatttttcagggttttttgttttgttttgaactttctttcgcatttttcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATTGGTCGTGCAGTGGGGTCTGCAAGTCAGTGGACAGGATGAAGCACATCCA

Basic information

species Oryza sativa
transcript LOC_Os01g65590.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G119265_T02 (Zea mays), 3'ss of exon 8
gtcaatctcagctatcgattcttttcatgatcatcttcctagctagtggtactactccagatcagaatttttcagggttttttgttttgttttgaactttctttcgcatttttcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATTGGTCGTGCAGTGGGGTCTGCAAGTCAGTGGACAGGATGAAGCACATCCA
                       |   | || |   |   ||| || |  ||  ||||    | |||   ||||    | | |    ||  | |    |      || | |       ||||| |||||||||||||||||||| |||||||||||||||||||| ||||| ||||||||||| || ||||| ||||| ||                     
----------------------gtgggtcatgaaactgacagccagcgtcacccctcctctcctgaacaattca--cctatatacactgcctagTGACTCTGACTGCGTGT-------GCAGACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACTGGTCGTGCAGCGGCGTCTGTAAGTCGGT---------------------

upper sequence: LOC_Os01g65590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G431006_T01 (Zea mays), 3'ss of exon 7
gtcaatctcagctatcgattcttttcatgatcatcttcctagctagtggtactactccagatcagaatttttca-----gggttttttgttttgt---tttgaactttctttcgcatttttcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATTGGTCGTGCAGTGGGGTCTGCAAGTCAGTGGACAGGATGA---AGCACATCCA
                |   | |   |    || | ||    |  | ||  |   ||| ||  |        ||     | |  |  ||  | |    | |||   |   | ||  | | ||    ||||| |||||||||||||||||||| || ||||||||||| ||||| |||||  |||||||||| || ||||||||||| | |||||||||||    ||||||   
--------------gtgggccatgaaactgacagcatcacctccggcggctccgttccggaataattcacaccaacggcgagcctgctgcatggcatctctgactgtgtgtgcgtgtgtgtcgtctgcagACTGCGAGTGGAAGAAGCGAGCCGGCAACGTGTGCGTAGCGTCCTTCGACGGGTCGTGCAGCGGCGTCTGCAAGTCGGCGGACAGGATGATGCGGCACAT---

upper sequence: LOC_Os01g65590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G119265_T01 (Zea mays), 3'ss of exon 8
gtcaatctcagctatcgattcttttcatgatcatcttcctagctagtggtactactccagatcagaatttttcagggttttttgttttgttttgaactttctttcgcatttttcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATTGGTCGTGCAGTGGGGTCTGCAAGTCAGTGGACAGGATGAAGCACATCCA
                       |   | || |   |   ||| || |  ||  ||||    | |||   ||||    | | |    ||  | |    |      || | |       ||||| |||||||||||||||||||| |||||||||||||||||||| ||||| ||||||||||| || ||||| ||||| |||||| |||||   ||||||||
----------------------gtgggtcatgaaactgacagccagcgtcacccctcctctcctgaacaattca--cctatatacactgcctagtgactctgactgcgtgt-------gcagACTGCGAGTGGAAGAAGCGAGCCGGGAACGTGTGCGTGGCGTCCTTCGACTGGTCGTGCAGCGGCGTCTGTAAGTCGGTGGACCGGATGCGCCACATCCA

upper sequence: LOC_Os01g65590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G36830.1 (Glycine max), 3'ss of exon 7
gtcaatctcagctatcgattcttttcatgatcatcttcctagctagtggtactactccagatca---gaatttttcagggttttttgttttgttttgaactttctttcgcatttttcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATTGGTCGTGCAGTGGGGTCTGCAAGTCAGTGGACAGGATGAAGCACATCCA
                            |  | | ||| | ||||||     |  |  ||| |    |||| ||  |    | | |  |||  ||     ||| | | |   |||  ||  |||||||| || ||||||    |  | || || ||||||||||| || || |||||||||||||||||  |||| ||||| ||||| || ||||   | || ||
----------------------------gtacgttttctttgctagttcacatcttatagagcgtacgaatattataaaaatatataatttcatt-----tttgtcttg---tttgtacacgcagATTGTGATTGGAAGGCAAGGACAGGAAATGTGTGCGTGGCATCTTTTGATTGGTCGTGCAGTGGTATCTGTAAGTCGGTGGAGAGAATGAGAGATATACA

upper sequence: LOC_Os01g65590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv18s0089g01040.t01 (Vitis vinifera), 3'ss of exon 7
gtcaatctcagctatcgattcttttcatgatcatcttcctagctagtggtactactccagatcagaatttttcagggttttttgttttgttttgaactttctttcgcatttttcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATTGGTCGTGCAGTGGGGTCTGCAAGTCAGTGGACAGGATGAAGCACATCCA
                |||| ||   |  || || |   ||  ||      ||| |  |  | |  | ||||    ||||||| |||| ||   ||  |    | | || |   |     ||||||||| |||||||  | || ||| || || || ||||| || || |||||||||||||||||  | |||||||| ||||| ||||||||| |  | ||
---------------tgatt-ttgctagaattatatatatatatat-----ctaatgaaagttactactttttgatgttttttttttttttcctaagataacgttggatgtga-atatttagATTGCGAATGGAAGACACAAGTTGGAAATGTATGTGTGGCATCCTTTGATTGGTCGTGCAGTGGAATATGCAAGTCTGTGGAGAGGATGAAGGATGTGCA

upper sequence: LOC_Os01g65590.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ20056 (Selaginella moellendorffii), 3'ss of exon 11
gtcaatctcagctatcgattcttttcatgatcatcttcctagctagtggtactactccagatcagaatttttcagggttttttgttttgttttgaactttctttcgcatttttcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATTGGTCGTGCAGTGGGGTCTGCAAGTCAGTGGACAGGATGAAGCACATCCA
                                                                     |     | | || |  || |      | |        | ||  |  ||  |||||||||||||||||   |  || ||||| | |||||| ||||||||||| ||||| ||||||||| | ||||||||||  || |||||  |  |  | ||
--------------------------------------------------------------------gtacgcagatcttctccttggaacaagattagaacgaactttcctttcttccagATTGCGAGTGGAAGGCACAGGCAGGGAATGCGTGCGTCGCGTCGTTCGACTGGTCTTGCAGTGGGATTTGCAAGTCAGCCGAGAGGATTCACGAAGTTCA

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|89188701|gb|CI115950.1|CI115950
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|88968716|gb|CI098882.1|CI098882
EST:     TCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: TCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|86482713|gb|CI125346.1|CI125346
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|88958160|gb|CI095679.1|CI095679
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|88967999|gb|CI098241.1|CI098241
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|86434226|gb|CI094569.1|CI094569
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|88956183|gb|CI092471.1|CI092471
EST:     ACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: ACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|88968290|gb|CI098532.1|CI098532
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|88956271|gb|CI092559.1|CI092559
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGNGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|86433236|gb|CI093579.1|CI093579
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|86535088|gb|CI175294.1|CI175294
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|27548070|gb|CA766088.2|CA766088
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|88222091|gb|CI222047.1|CI222047
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|89194693|gb|CI117130.1|CI117130
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|88958599|gb|CI096115.1|CI096115
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|88956397|gb|CI092666.1|CI092666
EST:     GCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGNGGCGTCGTTCGATT
genomic: GCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|86434003|gb|CI094346.1|CI094346
EST:     GGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGCGGCGTCGTTCGATT
genomic: GGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|86434155|gb|CI094498.1|CI094498
EST:     CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGCTCGATT
genomic: CGAGGTCGAGCACGTCGACGACCGCAGCATGTGCTGCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|88962205|gb|CI097358.1|CI097358
EST:     CGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: CGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
EST: gi|86483465|gb|CI126098.1|CI126098
EST:     GCGCCACGCCGCCAG                         ATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT
genomic: GCGCCACGCCGCCAGgtcaatctca ... tcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcagggttttttgttttgttttgaactttctttcgcatttttcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATTGGTCGTGCAGTGGGGTCTGCAAGTCAGTGGACAGGATGAAGCACATCCA
                             ctttctttcgcatttt  CT-rich tract
          ttttttgttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaatctcagctatcgattcttttcatgatcatcttcctagctagtggtactactccagatcagaatttttcagggttttttgttttgttttgaactttctttcgcatttttcactggcagATTGCGAGTGGAAGAAGCGAGCTGGGAACGTGTGCGTGGCGTCGTTCGATTGGTCGTGCAGTGGGGTCTGCAAGTCAGTGGACAGGATGAAGCACATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC