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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccatgttgtgatttcagaacaaatgccatctgactgtcgcgatctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g14860.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G024151_T01 (Zea mays), 5'ss of exon 3
GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccat---gttgtgatttcagaacaaatgc-catctgactgtcgcg-atctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcag
||||||||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||||||||  |||||||| || |||||||||| | | | |   |||    |  ||||||   ||| | |   ||| |   |   ||   ||||||  |  | || ||   | |||  | | | ||||  |||                        
GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACTGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgtgagtgctttactgcatttgatcatgatttatcaactattctacatgtttttagtgcatgtctgaatctaataattgagagtcaag--accataattt--aat------------------------

upper sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G835235_T04 (Zea mays), 5'ss of exon 3
GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccatgttgtgatttcagaacaaatgc-catctgactgtcgcgatctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcag
||||||||||| || || ||||| || || || || ||||| || |||||||||||||| |||||||||||||  |||||||| || ||||||| || | | | |   ||| |  | ||     ||||  ||  ||| |   |   ||| |||  |||     | |      ||||| |    |||   | | |||  | |                
GAAGTTGAAGCAACCATAATTAATGGGAAAGGGACCGAAACTGGGCACATAATTGTCACCACTACTGGTGGCAAGAATGGTCAACCAAAACAGgcgagtgctttactgcatttgattatc----aacagctgtgcatgtttttagtgcgttcttgaatcaaatagctg----aaagccaagaacataatttaatgagctac----------------
















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|58602831|gb|CK013359.1|CK013359
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         AGAGTTAGCTACATGGCTGAGCGTAT-GTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58685932|gb|CK074619.1|CK074619
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58661642|gb|CK050322.1|CK050322
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|2317492|gb|C22546.1|C22546
EST:     GGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58598975|gb|CK009503.1|CK009503
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58674441|gb|CK063127.1|CK063127
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58665294|gb|CK053980.1|CK053980
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58676495|gb|CK065182.1|CK065182
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58665103|gb|CK053789.1|CK053789
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|29687086|gb|CB683361.1|CB683361
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58664372|gb|CK053058.1|CK053058
EST:     CCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCAGAAACAG                         ACAGTTAGCTAC
genomic: CCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCC-GAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTAC
EST: gi|58673516|gb|CK062202.1|CK062202
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58652484|gb|CK041164.1|CK041164
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCG--A-A-                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58671331|gb|CK060017.1|CK060017
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58657986|gb|CK046666.1|CK046666
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58654229|gb|CK042909.1|CK042909
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCGGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58590979|gb|CF989287.1|CF989287
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58653056|gb|CK041736.1|CK041736
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|29618976|gb|CB623988.1|CB623988
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|58653567|gb|CK042247.1|CK042247
EST:     GACACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGGCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGG
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGG
EST: gi|163921584|gb|EG712155.1|EG712155
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|5003279|gb|AU068428.1|AU068428
EST:     CCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: CCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|86596734|gb|CI286647.1|CI286647
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
EST: gi|33796677|gb|CF324206.1|CF324206
EST:     GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAG                         ACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT
genomic: GCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATT

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: 75 (upstream exon), 60 (downstream exon)
Score: 78

GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcct ... aatcttgcagACAGTTAGCTACATGGCTGAGCGTATTGTAGGGCAAGGTTCATTTGGGATTGTCTTCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGTTGAAGCGACTATTATTAACGGCAAGGGAACAGAAACCGGCCACATAATTGTCACAACTACTGGTGGCAGAAATGGTCAGCCGAAACAGgtgatttcctgataccatgttgtgatttcagaacaaatgccatctgactgtcgcgatctgaaattgttcatcgattataaagcaatcttcatttctaattgatattcttggataatcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG