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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaatctagcctaaggtctgttgtctatactgcttccaactcatcagtttgtatttgggcactgctgactgtttaccatgcctgtgcccgtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT

Basic information

species Oryza sativa
transcript LOC_Os02g10720.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G180967_T02 (Zea mays), 3'ss of exon 3
taaaatctagcctaaggtctgttgtctatact-gcttccaactcatcagtttgtatttgggcactgc-tgactgtttaccatgcctgtgcccgtc-actgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT
|  |   | ||  |    | || |   || || | ||   |||    | || | |  | |   |||  || || |  | |   | | |||| | | |||||||||| ||||||||||| || ||||| || |||||| | || || || |||||| ||| ||||||||||
ttgatagtggcgcaccagcagt-gcgaatgctcgattaatacttccaaattagca--tagtttctgagtgcctttcgaactaacatttgcctggcgactgcagTTGTAATGCTACATACGAAAGCCTGCTCGGAAGCTCGAAGCCGTTCCCACAACCGACCCCTCTTGGT

upper sequence: LOC_Os02g10720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G497531_T01 (Zea mays), 3'ss of exon 3
taaaatctagcc-taaggtctgttgtctatactgcttccaactcatcagtttgtatttgggcactgctgactgtttaccatgcctgtgcccgtc-actgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT
     || |||  | ||   | |||| |||| | |||  || |  |  | | |  | ||    |   |      | |  ||   | |||  | | |||||||||| ||||||||||| |||||||| || || ||| | ||||||||||||||| ||||||||||||||
ggctctccagcagttagaaatcttgtttataatactttgaaatt-taggatagcttctgattgccttttgaaactaat-atctatctgcatggcgactgcagTTGTAATGCTACATACGAGAGCCTGCTCGGGAGCTCGAAACCATTTCCACAACCGATCCCTCTTGGT
















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|3766768|gb|AU030878.1|AU030878
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|12622897|gb|AU173110.1|AU173110
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|14192160|gb|AU184371.1|AU184371
EST:     AACAGAAGGCACAATTTTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTNTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|86512046|gb|CI154679.1|CI154679
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|29689717|gb|CB685992.1|CB685992
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|8324561|gb|AU091706.1|AU091706
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|14192107|gb|AU184318.1|AU184318
EST:     AACAGAAGGCACAATTTTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTNTAGGAAGCACAAAACCATTTCCNCA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|88975725|gb|CI023976.1|CI023976
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCCAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACGAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|3766735|gb|AU030845.1|AU030845
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|88282037|gb|CI403433.1|CI403433
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|32947923|gb|BP184495.1|BP184495
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|88199489|gb|CI199339.1|CI199339
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|88514176|gb|CI441682.1|CI441682
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|86853556|gb|CI329014.1|CI329014
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|4714360|gb|AU058327.1|AU058327
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|88984466|gb|CI015018.1|CI015018
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|86882289|gb|CI325747.1|CI325747
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|88297617|gb|CI550680.1|CI550680
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|86531003|gb|CI171209.1|CI171209
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|88297057|gb|CI542769.1|CI542769
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|44678412|gb|CR291846.1|CR291846
EST:     AACAGAAGGCACAATTCTCAGCTTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
EST: gi|88966152|gb|CI013028.1|CI013028
EST:     AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAG                         TTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA
genomic: AACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACA

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: 73 (upstream exon), 64 (downstream exon)
Score: 62

GACTTCTCCTGTGGAACCAGACTAGGCAACAGTGGGTTGGAAACAGAAGGCACAATTCTCAGCGTCAACAACCTCGAGAGCCAAAAATAAGgtattcatat ... gtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttgtatttgggcactgctgactgtttaccatgcctgtgcccgtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT
                  tgctgac  putative branch site (score: 62)
     tgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaatctagcctaaggtctgttgtctatactgcttccaactcatcagtttgtatttgggcactgctgactgtttaccatgcctgtgcccgtcactgcagTTGGAATGCTACATATGAGAGCCTTCTAGGAAGCACAAAACCATTTCCACAAGCGATCCCTCTTGGT

- - - - - - - - - ctgttgt
- - - - - - - - - - - - - - - -tgcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcct