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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaacgctcctgcttctcctcctattgtttgttcttcgaatttcgtgctttgcttgtggttggcccttctctgtggaggggaaatacggggaata...

Basic information

species Oryza sativa
transcript LOC_Os01g64690.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G09090.1 (Glycine max), 5'ss of exon 1
GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaacgctcctgcttctcctcctattgtttgttcttcgaatttcgtgctttgcttgtggttggcccttctctgtggagggga---aatacggggaata----
||  ||||||||||||||  ||||||| || |||||||||||||||||||| ||||| ||||| ||| | |||||| | ||||| || ||||| || || |||         || |   |||     | || ||| ||| || || ||  |   ||||||    ||   |  | | ||||           | ||   | ||     
GAGTGCGGTGAAGGAGCCTTTGGATCTCATTAGGCTCAGCCTCGACGAGCGTATCTATGTCAAACTCCGTTCCGACAGAGAGCTTCGTGGCAAACTTCACgta-------attcttcaatctttctttgtttttttttcctccaaatttctctgttgctttcttttaaactctttttgtgactaccctttgacacataggatgtttt

upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G28300.1 (Glycine max), 5'ss of exon 1
GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgta----tgtaaacgctcctgcttctcctccta------ttgtttgttcttcgaatttcgtgctttgcttgtggttggcccttctctgtggaggggaaatacggggaata
||  ||||||||||||||  ||||||| || |||||||||||||||||||| ||||| ||||| ||| | |||||| | ||||| || ||||| || || |||    |  || |  |  |  |||||||  |       |||| ||||  |  ||  |  |  ||| ||  |  |||   |||| || |   | | |             
GAGTGCGGTGAAGGAGCCTTTGGATCTCATTAGGCTCAGCCTCGACGAGCGTATCTATGTCAAACTCCGTTCCGACAGAGAGCTTCGTGGCAAACTTCACgtaattcttcaatcttttttttttctccttttcatgaatttgtctgtttctttaagctttttttttactcttt-ttgagacttccctttaacgcgtagggt---------

upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA10G23570.1 (Glycine max), 5'ss of exon 1
GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgt---aaacgctcctgcttctcctccta---ttgtttgttcttcgaatttcgtgctttgcttgtggttggcccttctctgtggaggggaaatacggggaata
|| ||| |||||||||||  || |||| ||  |||| |||||||||||||| ||||||||||||||| | || ||| | ||||| |||||||| || || |||  |   || |  |  | |||||  || |    || | | ||  |   |  ||||||  | ||| |  |     |   | |  | |  | |  |   ||     
GAGCGCTGTGAAGGAGCCTTTGAATCTCATATGGCTTAGCCTCGACGAGCGTATCTACGTCAAGCTCCGTTCTGACAGAGAGCTTCGCGGCAAACTTCACgtacttttcaatctttttttcttcttttcatgaatttctctattgctttcagctcgtgcact-ctttttttgaatacccatttacgcacagcatgttttgg-----

upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G76860.1 (Arabidopsis thaliana), 5'ss of exon 1
GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaacgc---tcctgctt--ctcctcctattgtttgttcttcgaatttcgtgctttgcttgtggttggcccttctctgtggaggggaaatacggggaata
   | | |||| |||||| || |||||||| ||||| || ||||||||| | ||||| ||||||||| |||| |||||||| || ||||||||||| || ||| ||   |      |||||||    |||   | |  |   |  |  || | |  | |   |   | ||| |      | | || |     | |  |  |    
AGCCACCGTGAGGGAGCCACTAGATCTGATTAGGCTGAGTCTCGACGAGAGAATCTATGTCAAGCTCCGGTCAGACCGCGAACTTCGCGGCAAGCTTCACgtacgttttcttgtgccctgcttagtaccttgaacttgtcactacttaaaatactcgttccacacatagttcgtttgaattt-tgtaactttattttgccg----

upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv18s0072g00710.t01 (Vitis vinifera), 5'ss of exon 1
GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaacgctcctgcttctc-ctcctattgtttgttcttcgaatttcgtgctttgcttgtggttggcccttctctgtggaggggaaatacggggaata----
|| ||| |||||||||||| ||||||| || || || |||||||||||||| ||||||||||||||| | |||||||| || ||||| ||||| || ||||||| |     |||||   |||| ||  | || ||| | |||| |  |  | | ||  | | |  |   |  || | | |       || | |      |     
GAGCGCAGTGAAGGAGCCGTTGGATCTCATAAGACTTAGCCTCGACGAGCGTATCTACGTCAAGCTCCGCTCCGACCGTGAACTCCGAGGCAAACTTCATgtattt---ttctcctttctctctctttttttttttttccttctacatatgcgtttaaccttt--tcaacgttttttttttcctttaaatttcttttcctgttat

upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S16_329V6.1 (Physcomitrella patens), 5'ss of exon 1
GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaacgctcctgcttctcctcctattgtttgttcttcgaatttcgtgctttgcttgtggttggcccttctctgtggaggggaaatacgg-ggaata-
 | ||| |||||||||||  ||||| ||||| | |||||  | |||||||||||||||||||||||  |||| ||||| ||||||||||| ||||| || ||| | |   | ||  ||||    |     ||||    |   |    |  |||   | | ||  |      ||   ||||     | | |   | ||||   
CAGCGCTGTGAAGGAGCCTTTGGATTTGATCCGACTCAGTTTGGACGAGCGCATCTACGTCAAGCTGCGGTCTGACCGGGAGCTCCGCGGGAAGCTGCACgtaag-atttggtcacgctttgggttg-ggtgttaaaacggtggtggttttgcgccggtggttatccaggttttgttgtgtgattggattgttgcggaacgt

upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ21250 (Selaginella moellendorffii), 5'ss of exon 1
GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaacgctcctgcttctcctcctattgtttgttcttcgaatttcgtgctttgcttgtggttggcccttctctgtggaggggaaatacggggaata
   ||| || ||||||||||| ||||| ||| |||||||||| |||||||| ||||||||||||||  |  ||||  | ||||||||||||||||| |||||| ||   |     |  |  |||  | |    || | |||||      |     |    || || || | || | |                       
CGGCGCTGTCAAGGAGCCGCTTGATCTCATCCGGCTCAGCCTGGACGAGCGGATCTACGTCAAGCTGCGCGCCGATAGAGAGCTCCGCGGCAAGCTACATgtaagtttccatagattttcatccatcaa--agttatacttcgggaagggactcatctgagttgtgggtctttgttttccag------------------

upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ12023 (Selaginella moellendorffii), 5'ss of exon 1
GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaacgctcctgcttctcctcctattgtttgttcttcgaatttcgtgctttgcttgtggttggcccttctctgtggaggggaaatacggggaata
   ||| || ||||||||||| ||||| ||| |||||||||| |||||||| ||||||||||||||  |  ||||  | |||||||| |||||||| |||||| ||   |     |  |  |||  | |    || | |||||      |     |    || || || | || | |                       
CGGCGCTGTCAAGGAGCCGCTTGATCTCATCCGGCTCAGCCTGGACGAGCGGATCTACGTCAAGCTGCGCGCCGATAGGGAGCTCCGAGGCAAGCTACATgtaagtttccatagattttcatccatcaa--agttatacttcgggaagggactcatctgagttgtgggtctttgttttccag------------------

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|88552429|gb|CI482435.1|CI482435
EST:     GCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88506337|gb|CI433843.1|CI433843
EST:     GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88529735|gb|CI458076.1|CI458076
EST:     GCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|89163418|gb|CI100308.1|CI100308
EST:     AAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: AAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88471442|gb|CI408713.1|CI408713
EST:     GCATTTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88521712|gb|CI448379.1|CI448379
EST:     GCATTTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|8528361|gb|AU093176.1|AU093176
EST:     GCNTCTACGTCAAGNTCAGGCCCGACCGNGAG-TCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88554838|gb|CI485047.1|CI485047
EST:     TCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: TCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88523672|gb|CI451520.1|CI451520
EST:     TCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: TCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88994793|gb|CI036374.1|CI036374
EST:     GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88547915|gb|CI478246.1|CI478246
EST:     TCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: TCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|12622952|gb|AU173165.1|AU173165
EST:     GCATNTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTNTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88526966|gb|CI455068.1|CI455068
EST:     CGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: CGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|25800894|gb|CA756855.1|CA756855
EST:     GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88529062|gb|CI456389.1|CI456389
EST:     GCATGTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|88266873|gb|CI368649.1|CI368649
EST:     GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|86530098|gb|CI170304.1|CI170304
EST:     GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|86432320|gb|CI085931.1|CI085931
EST:     GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
EST: gi|86418840|gb|CI053641.1|CI053641
EST:     GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCAT                         GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG
genomic: GCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTG

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: 74 (upstream exon), 65 (downstream exon)
Score: 21

GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaac ... ctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCGCGGTGAAGGAGCCGCTGGATCTGATCAGGCTCAGCCTCGACGAGCGCATCTACGTCAAGCTCAGGTCCGACCGCGAGCTCCGCGGCAAGCTCCATgtatgtaaacgctcctgcttctcctcctattgtttgttcttcgaatttcgtgctttgcttgtggttggcccttctctgtggaggggaaatacggggaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccttctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggagggg