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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatacttattcctgctttgatattttgttagaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgttcatctgttta...

Basic information

species Oryza sativa
transcript LOC_Os01g17430.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G378906_T01 (Zea mays), 5'ss of exon 2
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgta-catacttattcctgctttgatattttgttagaatgagtttactttgtcgtatgttatccgctccaagtt-ttgtagtctata---tttgttcatctgttta
||||||||||||||| |||||||||||||| |||||||| || || || || |||||||||||||| |||||||||||||||||||| |||||||| ||||||  || ||| |   | | |||   || ||    | |    |||   ||| || |  | |  | ||   ||| || |||  | ||   |||    | | | |  
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACGTGTGCAGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaatatgcttctctgtacattgcagttgtg---aagtatccttaaactgtagtctcctttatgatcagtgttattctagcatgtaaggtttaaataacgggt--

upper sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G011101_T01 (Zea mays), 5'ss of exon 2
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgta-catacttattcctgctttgatattttgttagaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgttcatctgttta
||||||||||||||| |||||||||||||| |||||||| || || || ||||||||||||||||| |||||||||||||||||||| |||||||| |||||| ||| ||| |   | | |||   || ||  | | |   || |       ||   | | | |   |    ||| || ||  | ||| | |       ||
AAATGATATTCACATCGACATCATGGATTACATCTCACCTGCTACCTGTGCTGATGTTACTTTCCGGAACATGTGGGCAGAATTTGAATGGGAAAATAAGgtaacatgcttctctgtacgttgcagttgtgaaatatttgtttcagcaaaatgttcttaaactgtagcctcctttatactcagt-tttatactagcacata

upper sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G23780.1 (Glycine max), 5'ss of exon 2
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatacttattcctgctttgatattttgtta-gaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgttcatctgttta--
||||||||| || |||||||||||||| || || || || ||| |||| ||||||||  | ||| | |  |||||||| || ||||||||||||||||||||| || ||  ||||| |||   |  || | || |  |      |    ||   |   |||  |  | |  |||| | | | | |      |  || || |  
AAATGATATCCATATTGACATCATGGACTACATTTCTCCTGCATCTTGTGCTGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatat-ctctttcctccttctctcattggctatgtttttaaccaaagggtaaaaaaatatg-gtgctaccttttcttgcccaaagcaaccccact-ttcatt

upper sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA07G00610.1 (Glycine max), 5'ss of exon 2
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatacttattcctgctttgatattttgttagaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgttcatctgttta--
||||||||| || |||||||||||||| || || || || ||| |||| || |||||  | ||| | |  |||||||| || |||||||||||||||||||||  |   | | |    | |   |||   |  |  |    | |    ||   |   |||  |  | |  |||| | |   | |     ||  || || |  
AAATGATATCCATATTGACATCATGGACTACATTTCTCCTGCATCTTGTGCCGATGTGGCATTCAGAACTATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatgtctctttcctctttctcccattggctatgtttttaatcaaaaggtaaaaaaatatg-gtgctatcttttcttgctcaaagcaactccact-ttcatt

upper sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G31490.1 (Arabidopsis thaliana), 5'ss of exon 3
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgta-catacttattcctgctttgatattttgttagaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgttcatctgttta
 || || || |||||||| |||||||| |||||||| || ||    ||| | || ||| ||||| | |  ||||||||||| ||||| |||||||||||||||   |||  |  |||  ||| | | | |       |  ||||  ||  | ||  | | |  | |  ||   |||     | ||||  ||||| |     
TAACGACATACACATTGATATCATGGACTATATCTCCCCTGCTGTGTGCTCAGAGGTTGCTTTCAGAACTATGTGGGCAGAGTTTGAATGGGAAAACAAGgtaatttaccgaaacct--tttaaaagtattaccttctttgtttgtttgtttgttagat-tttggtataaccattgcctgttgtatt-attcatgtcag--

upper sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv04s0008g02320.t01 (Vitis vinifera), 5'ss of exon 2
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacat-acttattcctgctttgatattttgttagaatgagtttactttgtcgtatgt-tatccgctccaagttttgtagtctatatttgttcatctgttta
 ||||| |||||||||||||||||||| || || || || ||   |||  |||||||  | ||| | |  ||||||||||| ||||| ||||||||||||||| || |  ||    | |||  ||  |||     ||||     |  |  ||  |||  ||   |   |   || | ||  |  ||  |  | || | |   
CAATGACATTCACATTGACATCATGGACTACATATCTCCTGCTGTTTGTACTGATGTGGCCTTCAGAACTATGTGGGCAGAGTTTGAATGGGAAAACAAGgtaaatcatctagctgtccttccatgattttcccaaatggtaacatctgatctaatgggtacttgaatctttttgtttataccttacatagttatttttg--

upper sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv09s0018g02080.t01 (Vitis vinifera), 5'ss of exon 2
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatacttattcctgctttgatattttgttagaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgttcatctgttta---
 ||||| || || ||||| || |||||||| || || || ||| | || ||||||||  | ||  | | ||||||||| || |||||||||||||||||||||| |   |  |  |  |||| |  ||  ||  ||| | | || ||  |  |  ||         |||||||   || ||   |||| | |  ||   |   
CAATGACATCCATATTGATATAATGGATTACATTTCTCCGGCATCCTGTGCTGATGTGGCATTTAGAACCATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtacgtctctcataata-tttgcttcttaatttcaat-actatatttattgatcggtctctttgagcaagtttcccagactgc-tttgataacatgaacatca

upper sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S168_28V6.1 (Physcomitrella patens), 5'ss of exon 3
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatacttattcctgctttgatattttgttagaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgt--tcatctgttta-
 ||||| |||||||||||||||||||| || ||||| || ||  | || ||||||||| | || || ||||||||||| || |||||||||||||||||||||  ||   ||||    |||| | |  |   ||  | | | |   ||||   ||  |   | |   |  |||   |     |  |||   ||      ||| 
GAATGACATTCACATTGACATCATGGACTACATCTCTCCTGCTTCATGTGCTGATGTTGCATTTCGCAACATGTGGGCTGAGTTTGAGTGGGAAAACAAGgtatctatcgattct---tttgttttgcttcaagtttcattctctcttgtttcatacttatccccgtatctttgacatcgccttgttgaaatcgaacaattat

upper sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S42_100V6.1 (Physcomitrella patens), 5'ss of exon 3
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatacttattcctgctttgatattt-------tgttagaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgttcatctgttta
 ||||| || || || |||||||||||||| |||||||| ||| |||| || |||||    ||| | ||||||||||| |||||||| |||||||||||||||    |  | ||    ||| | ||||       | ||  ||||| |  | || |  |  | ||||    |  |  ||  | |  || ||   |  | | |||   
GAATGACATACATATCGACATCATGGATTACATCTCACCTGCATCTTGTGCAGATGTCGTCTTCAGAAACATGTGGGCTGAATTTGAATGGGAAAACAAGgtaacctcacaatctcttttttacatttccccttttttttaaatgattcgatttcg--ggtttttataaattttatcttcag-aacctgtagaagaac-tatgt---

upper sequence: LOC_Os01g17430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S309_15V6.2 (Physcomitrella patens), 5'ss of exon 3
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatacttattcctgctttgatattttgttagaatgagtttactttgt--cgtatgttatccgctccaagttttgtagtctatatttgttcatctgttta
 |||||||| ||||||||||||||||| || ||| | || ||  | ||  ||||| |  ||||||| |||||||||||||| ||||| ||||| ||||||||||  |  |  ||||  |||  | |     || | |   ||   || ||  | || |||||    ||    |||||   || | |||    |    |   |
GAATGATATCCACATTGACATCATGGACTACATCGCTCCTGCCTCGTGTACTGATATAGCTTTCCGCAACATGTGGGCAGAGTTTGAATGGGAGAACAAGgtac-caagtgctcct-ttttattttggccgtaaattcgtttcgtttcgtatcctacgttattgattcagcattttgatctcgacattgacgctatcgaaaa

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|58680023|gb|CK068710.1|CK068710
EST:     CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAG                         GTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
EST: gi|66927274|gb|CX114122.1|CX114122
EST:     CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAG                         GTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAG-TTTTGGATCATATC
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
EST: gi|218487976|gb|FG959847.1|FG959847
EST:     CTGATGTTACTTTCCGTGACATGTGGGCAGAATTTGAGTGGGAAAACAAG                         GTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
EST: gi|88211809|gb|CI211449.1|CI211449
EST:     CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAG                         GTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
EST: gi|13420668|gb|AU174758.1|AU174758
EST:     CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAG                         GTGGCAGTGAATACTGTCATTCAGAATGAGA
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGA
EST: gi|88691409|gb|CI733487.1|CI733487
EST:     CTGATGTTACTTTCCGTAACATGTGGGCAGAATTCGAGTGGGAAAACAAG                         GTGGCAGTGAATACTGTCATTCACAATGAGAAGGAGTTCTTGGATCATATC
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
EST: gi|86250680|gb|CI003798.1|CI003798
EST:     CTGATGTTACTTTCCGTAACATGTGGCCAGAATTTGAGTGGGAAAACAAG                         GTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
EST: gi|24468792|gb|CA305741.1|CA305741
EST:     CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAG                         GTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
EST: gi|86478084|gb|CI120717.1|CI120717
EST:     CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAG                         GTGCCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
EST: gi|7212766|gb|D40362.2|D40362
EST:     CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAG                         GTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGGATCATAT
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGG-ATCATAT
EST: gi|86827314|gb|CI270964.1|CI270964
EST:     CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAG                         GTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC
genomic: CTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATC

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), 74 (downstream exon)
Score: 77

AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatactt ... cattcatcagGTGGCAGTGAATACTGTCATTCAGAATGAGAAGGAGTTTTTGGATCATATCATCAAGTCAACAAACATGAAGTGTCTAACACCACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGATATTCACATTGACATCATGGATTATATCTCACCAGCAACTTGCGCTGATGTTACTTTCCGTAACATGTGGGCAGAATTTGAGTGGGAAAACAAGgtacatacttattcctgctttgatattttgttagaatgagtttactttgtcgtatgttatccgctccaagttttgtagtctatatttgttcatctgttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgctcc