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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCGACGGCTACGCGCACCTCTCCTCCGGCCTCGCGTGCGGCCTCGCCGGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatccccatcccgaaatcccccccacccaaaatgtgttaaactttttttgatgtggatttgttaataatactccggaatgaggtaaaattgctgaact...

Basic information

species Oryza sativa
transcript LOC_Os02g34510.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g34510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G893252_T01 (Zea mays), 5'ss of exon 2
TCTTCGACGGCTACGCGCACCTCTCCTCCGGCCTCGCGTGCGGCCTCGCCGGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatccccatcccgaaatcccccccacccaaaatgtgt-taaactttttttgatgtggatttgttaataatactccggaatgagg-taaaattgctgaact
||||||||||||||||||||||||||||||| ||||| ||||||||||| |||||||| ||||| |||||||||||||||||||| |||||||| || |||| |     || |    ||  |     || |   | |||  |      |  | ||      |     | || |  | |     ||| | | |      || |
TCTTCGACGGCTACGCGCACCTCTCCTCCGGACTCGCCTGCGGCCTCGCTGGCCTCGCTGCCGGCATGGCCATCGGCATCGTCGGAGACGCCGGAGTTAGgt-actgtaatactctgattgcagttgcc-atcctttgtacatgtccatgctaattgattctcagggaaaaaaaactgtcgccaggcttagaccaagcaatt

upper sequence: LOC_Os02g34510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA11G07980.1 (Glycine max), 5'ss of exon 1
TCTTCGACGGCTACGCGCACCTCTCCTCCGGCCTCGCGTGCGGCCTCGCCGGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatccccatc----ccgaaatcccccccacccaaaatgtgttaaactttt---tttgatgtggatttgt-taataatactccggaatgaggtaaaattgctgaact
|||||||||||||||| |||||||||||||||||||| ||||||||||| |||||| |||| || |||||||| ||||| || ||||| ||||| || ||||  || |  ||     | |  |  |     |     |  | | | |   |    |  |||| | ||   | |||| ||  ||  |  |  ||| |  |         
TCTTCGACGGCTACGCTCACCTCTCCTCCGGCCTCGCTTGCGGCCTCGCTGGCCTCTCCGCTGGCATGGCCATTGGCATTGTTGGCGATGCCGGTGTTAGgtattctcactcattttctatttttctttttctttttacttataacatgatcgaataagatgcgtatagttataattattttcttgcgtatggttaggta--------

upper sequence: LOC_Os02g34510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G05630.1 (Glycine max), 5'ss of exon 2
TCTTCGACGGCTACGCGCACCTCTCCTCCGGCCTCGCGTGCGGCCTCGCCGGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatccccatcccgaaatcccccccacccaaaatgtgttaaactttttttgatgtggatttgttaataatactccgg-aatgaggtaaaat-tgctgaact---
|||| ||||| |||||||||||||| || || ||||| || |||||||| |||||| |||| || ||||||||||||||||| ||||| ||||| || ||||  ||  ||| |  |||| |   | | |    |  ||||     |  ||   | ||  ||   ||||  |  |      ||| | |    | |  || | |   
TCTTTGACGGTTACGCGCACCTCTCTTCGGGTCTCGCTTGTGGCCTCGCTGGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattcatcattc--aaattcaatcaagcttcgagttgttgctgctgctt---tatgctttcactaatgctgtttgattgatgtgctggtgtgttttgtaattca

upper sequence: LOC_Os02g34510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G24220.1 (Glycine max), 5'ss of exon 2
TCTTCGACGGCTACGCGCACCTCTCCTCCGGCCTCGCGTGCGGCCTCGCCGGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatccccatcccgaaatcccccccacccaaaatgtgttaaactttttttgatgtggatttgttaataatactccggaatgaggtaaaattgctgaact----
| || ||||||||||| |||||||| || || ||||| || |||||||| |||||| |||| || ||||||||||||||||| ||||| ||||| || ||||  ||  |||    |  |   |      | |  | |  |      |  || ||||   ||  |||||  | |    |  ||  ||    ||| ||   |    
TTTTTGACGGCTACGCCCACCTCTCTTCAGGTCTCGCTTGTGGCCTCGCTGGCCTCTCCGCTGGCATGGCCATCGGCATCGTTGGCGATGCCGGTGTTAGgtattcatcatttaaatttaatcatgcttcgagttattgttgctgctgctttatgtt--ttcattaatgttgcat--gcttgttgtttggttgatgggttgagt

upper sequence: LOC_Os02g34510.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA01G37320.1 (Glycine max), 5'ss of exon 1
TCTTCGACGGCTACGCGCACCTCTCCTCCGGCCTCGCGTGCGGCCTCGCCGGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatccccatcccgaaatcccccccacccaaaatgtgttaaactttttttgatgtggatttgttaataatactccggaatgaggtaaaattgctgaact-------
|||||||||||||||| |||||||||||||||||| | ||||| || || |||||| |||| || |||||||| ||||| || ||||||||||| || |||| || | ||  ||    | |  | | | |    | | |  ||     |     ||| | || | ||| ||  ||  | ||  |||    |   ||           
TCTTCGACGGCTACGCTCACCTCTCCTCCGGCCTCTCTTGCGGTCTTGCTGGCCTCTCCGCTGGCATGGCCATTGGCATTGTTGGCGACGCCGGTGTTAGgt-attctcactcctt--ttctactctctctttttctttcgaaaaagat---gcgtgtagttat-aattattttcttgcatatggtttggtatttggttcaaggcca

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|86893602|gb|CI314757.1|CI314757
EST:     GCCTCGCCGTCC-GGAT-GCCAACGGCATCGTCGACGACGCCGGCGTCAG                         GGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
genomic: GCCTCGCCG-CCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatcccca ... ttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
EST: gi|58695580|gb|CK084267.1|CK084267
EST:     GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAG                         GGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
genomic: GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatcccca ... ttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
EST: gi|3761295|gb|C98543.1|C98543
EST:     GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAG                         GGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
genomic: GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatcccca ... ttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
EST: gi|88467293|gb|CI696667.1|CI696667
EST:     GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAG                         GGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCT
genomic: GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatcccca ... ttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCT
EST: gi|58600175|gb|CK010703.1|CK010703
EST:     GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAG                         GGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
genomic: GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatcccca ... ttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
EST: gi|29683824|gb|CB680099.1|CB680099
EST:     GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAG                         GGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
genomic: GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatcccca ... ttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
EST: gi|14192323|gb|AU184534.1|AU184534
EST:     GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAG                         GGCAAATGCTCAACAGCCAAAACTGTTTGNGGGTATGATCCTCA
genomic: GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatcccca ... ttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCA
EST: gi|88977585|gb|CI025321.1|CI025321
EST:     GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAG                         GGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
genomic: GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatcccca ... ttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
EST: gi|29683825|gb|CB680100.1|CB680100
EST:     GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAG                         GGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT
genomic: GGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatcccca ... ttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTAT

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: 70 (upstream exon), 41 (downstream exon)
Score: 14

TCTTCGACGGCTACGCGCACCTCTCCTCCGGCCTCGCGTGCGGCCTCGCCGGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatcccca ... ttgctctcagGGCAAATGCTCAACAGCCAAAACTGTTTGTGGGTATGATCCTCATCCTTATCTTTGCGGAAGCGCTTGCACTCTATGGTCTCATTGTTGGTATCATCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCGACGGCTACGCGCACCTCTCCTCCGGCCTCGCGTGCGGCCTCGCCGGCCTCGCCGCCGGGATGGCCATCGGCATCGTCGGCGACGCCGGCGTCAGgttatccccatcccgaaatcccccccacccaaaatgtgttaaactttttttgatgtggatttgttaataatactccggaatgaggtaaaattgctgaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc