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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgacatttgaaaccccgctcattagaaggttgcgtattattgctatttattcctccatcgagcttcatctaaaaacatatatgtttccctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAATCAATTTGCGGTTGGGCTTTCAGATGGATCTGTTAAAGTGATTGAACCC

Basic information

species Oryza sativa
transcript LOC_Os01g15020.2
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 24
----ttttgacatttgaaaccccgctcattagaaggttgcgtattattgctatttattcctccatcgagcttcatctaaaaacatatatgtttccctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAATCAATTTGCGGTTGGGCTTTCAGATGGATCTGTTAAAGTGATTGAACCC
     ||   ||||   |   |  | |||       |   |   |||     ||   ||   ||    |   || ||||  | || | ||||||      ||||||||||| | ||  |||||||||||||||| |||||||| || ||| | || ||||||||||| ||||| |||||||| || || |||||| | || || 
atagattacccattcatattgcaacacatattgtcatgatgccatatgatccttatatctaacactagg---cacctaagta-atgtctgtttcatgattccagCAATCCACCTGTTCACCCTCTTGTCGTCGCCGCACATCCCCACGAGCCAAACCAATTTGCGGTCGGGCTGTCAGATGGGTCCGTCAAAGTGCTGGAGCCA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 22
-ttttgacatttgaaaccccgctcattagaaggttgcgtattattgctatttattcctccatcgagcttcatctaaaaacatatatgtttccctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAATCAATTTGCGGTTGGGCTTTCAGATGGATCTGTTAAAGTGATTGAACCC
    |||  ||||||         ||       |    |  |   | ||    |   |  | |      || |||| || || ||||||||  |   |||||||||||   ||  |||||||||| ||||| |||||||| || ||| | || ||||||||||| ||||| |||||||| |  ||||||||| | || || 
agagtgatgtttgaatatggatatatagatgaataaactgctggagatagccttatatatagcaccaggcacctaagaa-atgtatgtttcattattccagCAATCCACATGTTCACCCTCTTGTTGTCGCCGCACATCCGCACGAGCCAAACCAATTTGCGGTGGGGCTGTCAGATGGGTTCGTTAAAGTGCTGGAGCCA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 24
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 24
ttttgacatttgaaaccccgctcattagaaggtt-gcgta---ttattgctatttattcctccatcgagcttcatctaaa---aacata-tatgtttccctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAATCAATTTGCGGTTGGGCTTTCAGATGGATCTGTTAAAGTGATTGAACCC---
                 |||    ||| ||  ||    ||   ||  |   ||  ||    |||| | | ||  |    |   |  ||  | | |||  || |      | | || || | | ||| |  ||  || | || |||||||| ||  |||||||||| |||||||| || || ||||| || |||||||||||||| ||    
--------------gtaccgtattttacaaacttcatataaagtttatatcatccatctgaccattgtgattttttgggactgattatgctttctttttcttctgtgatagTGCACCGATTTTCCCACAGGTGATCACAGCTCATCCACAAGAACCGAATCAATTAGCGGTTGGACTGTCTGATGGTTCGGTTAAAGTGATTGAGCCATCA

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|38481037|gb|CF965126.1|CF965126
EST:     TTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: TTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|87009996|gb|CI277497.1|CI277497
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|86597087|gb|CI272682.1|CI272682
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|87020791|gb|CI269508.1|CI269508
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|88459574|gb|CI519635.1|CI519635
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|86827714|gb|CI272943.1|CI272943
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|29630394|gb|CB635403.1|CB635403
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|89184043|gb|CI046608.1|CI046608
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|86843194|gb|CI341352.1|CI341352
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|58680385|gb|CK069072.1|CK069072
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGT
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGT
EST: gi|88234089|gb|CI233938.1|CI233938
EST:     CCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: CCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|88282501|gb|CI403897.1|CI403897
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|58675235|gb|CK063922.1|CK063922
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|88729944|gb|CI753165.1|CI753165
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|87039523|gb|CI194145.1|CI194145
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|86477786|gb|CI120419.1|CI120419
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|88382227|gb|CI533431.1|CI533431
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCNTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|88296043|gb|CI535206.1|CI535206
EST:     ACCTCCAGCATACTTATCTTCTGCAGCCATAAACAC                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: ACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|88481634|gb|CI418905.1|CI418905
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|58677680|gb|CK066367.1|CK066367
EST:     CAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: CAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|88478632|gb|CI415903.1|CI415903
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|29626132|gb|CB631143.1|CB631143
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|86482317|gb|CI124950.1|CI124950
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|25803958|gb|CA759919.1|CA759919
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCGTAAACAG                         CAATCCATCGGTCTACCCTCTNGTTGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|29630453|gb|CB635462.1|CB635462
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
EST: gi|86900308|gb|CI296351.1|CI296351
EST:     AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAG                         CAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA
genomic: AGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAA

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), 75 (downstream exon)
Score: 61

CCTTTACCGATGGTAACATAGGAATTTTTGATGTGGAGAACTTGAGATTAAGATGCCGAATTGCACCTCCAGCATACTTATCTTCTGCAGCCATAAACAGgtactcacta ... cctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAATCAATTTGCGGTTGGGCTTTCAGATGGATCTGTTAAAGTGATTGAACCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttattcctccatcgagcttcatctaaaaacatatatgtttccctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAATCAATTTGCGGTTGGGCTTTCAGATGGATCTGTTAAAGTGATTGAACCC
                        atctaaa  putative branch site (score: 61)
                                       tgtttccct  putative PPT
                           taaaaacatatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgacatttgaaaccccgctcattagaaggttgcgtattattgctatttattcctccatcgagcttcatctaaaaacatatatgtttccctgcaccagCAATCCATCGGTCTACCCTCTTGTCGTCGCTGCACATCCACAGGAGTCGAATCAATTTGCGGTTGGGCTTTCAGATGGATCTGTTAAAGTGATTGAACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA