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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctctgtgttcttgctggacaactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa...

Basic information

species Oryza sativa
transcript LOC_Os04g51610.1
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 28
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctctgtgttcttgctggacaactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaa-atgaa--
| ||||||||||||||||| ||||||||| ||||||| |||||| |||||||||||||||||||  ||||||||||| ||||||| ||||| || |||||||      ||    |   |  || |  | ||| |    || | | ||    ||| || |   | | | | |||    || ||  |  | || | | ||  |  
TGCTGTGGGTTAACCTAATTATGGATACTTTGGGTGCCCTTGCATTGGCGACAGAACCACCTACAAACCATCTTATGGAGAGACCCCCAGTAGGGAGAAGgtagtgaatcaccatctatcttgtagcattgtttaaactg-tgtatgttcgtaaattgtac-acactac-tttctctgatcacaattccattggacattgaca

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G391042_T01 (Zea mays), 5'ss of exon 28
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctctgtgttcttgctggacaactgtcttgcttggtttct---ggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa-
|  |||||||||||||||| ||||| ||| ||||||| |||||| |||||||||||||||||||  ||||||||||| ||||||| ||||| || |||||||||||||| ||||  | ||||  | |  || ||  | | || |||    |||| |      | | ||     | |           |    || || |||   
TGTTGTGGGTTAACCTAATTATGGACACTTTGGGTGCCCTTGCATTGGCGACAGAACCACCTACAAACCATCTTATGGAGAGACCCCCAGTAGGGAGAAGgtttgttct-tgtgcacgtgct--atatttg-ctcacctagtatcttatagagagaccccagtagggagaaggtatctgattggcaaatattatggacatggca

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA15G00340.1 (Glycine max), 5'ss of exon 29
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctctgtgttcttgctggacaactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa
|  ||||||| ||| | |||||||| || || || |||||||||||||| || ||||| || || ||| | |||||||| ||| ||||||||||| |||||||||||     | || || |     ||  |      | || ||    | ||  | | |||| | |||||                              
TTTTGTGGGTCAACGTTATCATGGACACACTTGGGGCTCTTGCACTGGCTACGGAACCGCCAACAGACAACCTTATGCACAGATCACCAGTTGGCCGAAGgtttgtttggctttttatttcaaattaaaagcagacttgggcttactaacatcttatgtttg-gctttcag-----------------------------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA07G00630.2 (Glycine max), 5'ss of exon 27
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttg---ttctctgtgttcttgctggacaact--gtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa
|  ||||||| ||||| ||||||||||| || || || ||||||||||| || ||||| || || ||||  || ||||| ||| ||||||||||| |||||||||   |  |  |  ||||  ||   ||  |   | ||  | |    ||  | |  ||  |  | ||    ||   ||| || || |  |   |  |  ||  
TTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattgattggctttctctctaagcagtttaatatttatggtacccttaatactatactgatcag----cacaaaaacgagcatgcacatgtacacttgg-

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA08G23760.1 (Glycine max), 5'ss of exon 30
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttg---ttctctgtgttcttgctggacaact--gtcttgcttggtttctggagat----aatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa
|  ||||||||||||| ||||||||||| || || || ||||||||||| || |||||||| || ||||  || ||||| ||| ||||||||||| |||||||||   |  |  |  ||||  ||   ||  |   | ||  | |  | || || |     || | |  |||  |  ||  |||| | ||| || |   |         
TTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAAGgtttggattgattggctttctcacttagcagtttaatatttatagtatccttgaaagttaaaactatactgatctagcacataaatgcacatgaacatgt---------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: GLYMA13G44990.1 (Glycine max), 5'ss of exon 29
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc-tgtgttcttgctggacaactgtct-tgcttgg----tttctggagataattttt-ttgagatttc----att-taaaggaacaggacccgatcgaaatgaa-----------------------------------------------------------
|  ||||||| ||||| |||||||| || || || |||||||||||||| || ||||| || || ||| | |||||||| ||| ||||||||||| ||||||||| | |  | || | |   ||||   ||  || | ||  |    ||| |    ||  ||||| |||  |||||    ||| || |  |||| |      || ||||  |                                                           
TTTTGTGGGTCAACCTTATCATGGACACACTTGGGGCTCTTGCACTGGCTACGGAACCGCCAACAGACAACCTTATGCACAGATCACCAGTTGGCCGAAGgtttggtttggtttggtttgattggatctcttactatactatgagaatttatacgcattttttttattgcaatttctaaaattatacaaaaacaaggtt-attcaaaatccaaatactcacttgaagacagacttgggcttactacgatatatcttatgtttggctttcag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 5'ss of exon 27
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctctgtgttcttgctggacaactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa--------
| || ||||| ||||| |||||||||||||| || || |||||||| || ||||| ||||| || || ||||||||||| ||| | || ||||| ||||||| |   |    ||  | || ||     ||       || ||        ||| || | ||| | ||||| |   | |    |     | | |               
TGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAAGgtataaacatgttgcacatgatgttttcctcatacttttagtgaaacagaatagttatattgtggtttcagtcgtatggttcgtgatggtttgtttcttgatttgcag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 29
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc-------tgtgttcttgctggacaactgtcttgcttggtttctggagataatttttttga-gatttcatttaaaggaacaggacccgatcgaaatgaa
| || ||||||||||| |||||||||||||| || || |||||| |||| || |||||||| ||||| ||||||||| | ||| | ||||||||  ||||||| |  ||        | |  |  |  ||      |  || |  |  |||    |  |   |||| ||| |  ||  |||         ||  | |||         
TTCTATGGGTTAACCTTATCATGGATACTCTTGGAGCACTTGCATTGGCTACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAAGgttagaacttgaagtagtatacttctcgtgattttgttcctcgtctaattttataatttggattttatgatgggttgttttcgtatggttgggactgatg--------

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 28
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 30
TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtt-tgttctctgtgttcttgctggac-----aactgtcttgcttggtttctggagataatttttttgagatttcatttaaaggaacaggacccgatcgaaatgaa
| || |||||||| || |||||||||||||| || || |||||| |||| || |||||||| || || || || ||||| || || ||||||||  ||||||  | || | | |  | |||   ||      || |    |   |    |  |  || ||||   |      |     |  |||          | |  |      
TCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAGgtaattttttttttaatgttgggagatccaataaatactgtttataaactaagtggaaaattgggtcagatctgtccctggaggtttgaattgtgcttca------

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|86514508|gb|CI157141.1|CI157141
EST:     AGTTGGCAGAAG                         GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
genomic: AGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
EST: gi|88351169|gb|CI623391.1|CI623391
EST:     ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGGAGAAG                         GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGG
genomic: ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATGG
EST: gi|29685708|gb|CB681983.1|CB681983
EST:     ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAG                         GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
genomic: ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
EST: gi|87027607|gb|CI272372.1|CI272372
EST:     ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAG                         GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
genomic: ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
EST: gi|58594188|gb|CF992496.1|CF992496
EST:     CAGAACCACCTACTGACCATCTTATGCCAGAGACCACCAGTTGGCAGAAG                         GGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
genomic: CAGAACCACCTACTGACCATCTTATGC-AGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG
EST: gi|218500877|gb|FG965670.1|FG965670
EST:     ACAGAACCACCTACTGACCATCTTATGCAGAGACCAACAGTTGGCAGAAG                         GGAACCCTTGAATAACAAATGTCATGTGGAGAAACTTAATCATAATG
genomic: ACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGA-TAACAAATGTCATGTGGAGAAACTTAATCATAATG

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: 43 (upstream exon), 74 (downstream exon)
Score: 35

TACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAAGgtttgttctc ... ttgttttcagGGAACCCTTGATAACAAATGTCATGTGGAGAAACTTAATCATAATG




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