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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttcccgagccataacttctccactgtaacagggttgtactttcgtttagaccttttgttgttatatcaatacaagaaatgatagttgtttattgt...

Basic information

species Oryza sativa
transcript LOC_Os09g32800.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32800.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G074386_T02 (Zea mays), 5'ss of exon 3
AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttcccgagccataacttctccactgtaacagggttgtactttcgtttag--accttttgttgttatatcaatacaagaaatgata-gttgtttattgt-------------------------------------------
                    ||||||| ||||| || |||||||| |||||||||||||||||| | |||||||||||||||||||       | | | ||||   |   |  ||  |  || ||  ||| ||     ||| ||| |  | ||| |||      | || |   |   |  | ||                                            
--------------------CATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaattacaactaaaactcagcttgta-aattgttttatatgttcattctatcaccctttttgttgataccaagcggttatatcaagcgccataaactgcaccagtactgattcaatagtatctttcatttgtctgtatatag

upper sequence: LOC_Os09g32800.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G074386_T01 (Zea mays), 5'ss of exon 3
AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttcccgagccataacttctccactgtaacagggttgtactttcgtttag--accttttgttgttatatcaatacaagaaatgata-gttgtttattgt-------------------------------------------
 || |||||||| | |||||||||||| ||||| || |||||||| |||||||||||||||||| | |||||||||||||||||||       | | | ||||   |   |  ||  |  || ||  ||| ||     ||| ||| |  | ||| |||      | || |   |   |  | ||                                            
GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaattacaactaaaactcagcttgta-aattgttttatatgttcattctatcaccctttttgttgataccaagcggttatatcaagcgccataaactgcaccagtactgattcaatagtatctttcatttgtctgtatatag

upper sequence: LOC_Os09g32800.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G817037_T02 (Zea mays), 5'ss of exon 3
AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttcccgagccataacttctc--cactgtaacagggttgtactttcgtttag--accttttgttgttatatcaa-----tacaagaaatga--tagttgtttattgt--------------------------------------------------
 || |||||||| | ||| |||||||| ||||| ||||||||||| || |||||||| |||||| | |||||||||||||||||||  |    | | |   | | ||  |     ||  |  || ||  ||| ||     | | ||| || |||||||||     | |   | || |   ||      | | |                                                  
GGCTGACAAATGTGTACTGGCATCTTCTGGCTTTCAAGGTGATATTAAGGCTCTGCAGAAGAACCTAGCTGCCAGAGAATTGgtaaaatttacaacaaactcctatcagcgtctaaattgttttatatgttcattctaccatcctttttttttatatcaagcagttcccttatatcaagcagacaggcactataaactgcaccagcactgatacgatattgtctttcatttgtttgtatatag

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|33804936|gb|CF328345.1|CF328345
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|58599894|gb|CK010422.1|CK010422
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCGCAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|218499612|gb|FG949767.1|FG949767
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCGCAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|33818104|gb|CF334878.1|CF334878
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|38472549|gb|CF956681.1|CF956681
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCGCAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|33678412|gb|CF306651.1|CF306651
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|33660627|gb|CF291594.1|CF291594
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|33683337|gb|CF311576.1|CF311576
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|38477362|gb|CF961495.1|CF961495
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCGCAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|58694905|gb|CK083592.1|CK083592
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCGCAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|55439808|gb|CV733214.1|CV733214
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|33681495|gb|CF309734.1|CF309734
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|33683521|gb|CF311760.1|CF311760
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|66915431|gb|CX102279.1|CX102279
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCGCAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|58593878|gb|CF992186.1|CF992186
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCGCAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|86592540|gb|CI253221.1|CI253221
EST:     ACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: ACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|55413999|gb|CV726375.1|CV726375
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|218497460|gb|FG955186.1|FG955186
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCGCAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|87023706|gb|CI286457.1|CI286457
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|33823301|gb|CF337451.1|CF337451
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCGGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|33803800|gb|CF327774.1|CF327774
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|86593079|gb|CI255541.1|CI255541
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|86503207|gb|CI145840.1|CI145840
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|56158103|gb|C73010.2|C73010
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|87035374|gb|CI189996.1|CI189996
EST:     AGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: AGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|58667664|gb|CK056350.1|CK056350
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCGCAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|55412184|gb|CV724560.1|CV724560
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
EST: gi|58674446|gb|CK063132.1|CK063132
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCT
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCT
EST: gi|33818151|gb|CF334904.1|CF334904
EST:     TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTG                         CTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA
genomic: TCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAA

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), 75 (downstream exon)
Score: 73

AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttccc ... gtttttgtagCTGTACCAGCACCAGCACAATAAAAGGATGAGCTGCCCTGCCATGGCACAACTGCTCTCCAACACTCTGTACTACAAGCGATTCTTCCCATATTATGCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttcccgagccataacttctccactgtaacagggttgtactttcgtttagaccttttgttgttatatcaatacaagaaatgatagttgtttattgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctcc