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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagccatctaattgattttctaaaaatagcttggccttttgaaatctctggatgcgcttgttcatttcagatagattctatgtgctgaatacattacagttgttacattgatgaatcatcatacatgtgcaaagcccatgtcttgctgatctcacataatttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGTAACTGTGTCAAGCGAGTGGTGGTCATTGTGACATCCGTTCTGTTCTTCC

Basic information

species Oryza sativa
transcript LOC_Os09g12600.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12600.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G047404_T01 (Zea mays), 3'ss of exon 7
gtcagccatctaattgattttctaaaaatagcttggccttttgaaatctctggatgcgcttgttcatttcagatagattctatgtgctgaat-acattacagttgttacattgatgaat--catcatacatg-tgcaaagcccatgtcttgctgatctcacat--aatttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGTAACTGTGTCAAGCGAGTGGTGGTCATTGTGACATCCGTTCTGTTCTTCC
| | | | | || || || | |||||| || || | || || | | ||||| | | | | | | | ||| | | | || || | | || | | | | ||||| |||||||| || ||||||||||| || || || ||||| || || || || ||||| || || |||||||| ||||||||||||||||| || ||||||||||||
------------------------gtggtgatccatcttgctaatattggtgtatttatctattcatt--gattacatcattaatgttggttcagattactatgtatgcctgtacaagttccatttcaaacaattcatagttcgcctactgatcttattgttttaaatttgttgaagGTATCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCTGTTCTGTTCTTCA

upper sequence: LOC_Os09g12600.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G103047_T01 (Zea mays), 3'ss of exon 7
gtcagccatctaattgattttctaaaaatagcttggccttttgaaatctctggatgcgcttgttcatttcagatagattctatgtgctgaat-acattacagttgttacattgatgaat--catcatacatg-tgcaaagcccatgtcttgctgatctcacat--aatttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGTAACTGTGTCAAGCGAGTGGTGGTCATTGTGACATCCGTTCTGTTCTTCC
| | | ||| || ||||| | |||||| || || | | || ||| | | ||||| || | | || || | | ||| | | | | || || | || | | | | | ||||||||||||||||| ||||||||||| || || || ||||| || || || || ||||| || || |||||||| ||||||||||||||||| || ||||||||||||
------------------------gtggtgatccatcttgctgatattggtggatttgtttgttc--tttgattacgtcatcaatgttgattcagattactgtatatgcctttataagttccatttgaaacaatttatagttcacctactgatcttattattttcaatttcttgaagGTGTCATACATGATCCTCGCCAGGGTATCCCCAGTCACACATTCAGTGGGCAATTGCGTCAAGCGTGTGGTGGTCATTGTGACCTCGGTTCTGTTCTTCA
















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|15853695|gb|BI806491.1|BI806491
EST:     TATACACAA-GTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|66913098|gb|CX099946.1|CX099946
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|27577402|gb|CB000097.1|CB000097
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|88205053|gb|CI204902.1|CI204902
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|163923308|gb|EG709363.1|EG709363
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|89180351|gb|CI044630.1|CI044630
EST:     ATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: ATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|58680478|gb|CK069165.1|CK069165
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|218492959|gb|FG966646.1|FG966646
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|86828012|gb|CI274919.1|CI274919
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|88243092|gb|CI244214.1|CI244214
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|88214697|gb|CI214546.1|CI214546
EST:     TTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|86499468|gb|CI142101.1|CI142101
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|33675431|gb|CF303670.1|CF303670
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|86498395|gb|CI141028.1|CI141028
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|163929491|gb|EG709282.1|EG709282
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|58668471|gb|CK057157.1|CK057157
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|27577441|gb|CB000136.1|CB000136
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|33674890|gb|CF303129.1|CF303129
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
EST: gi|88248370|gb|CI248219.1|CI248219
EST:     TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG                         GTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT
genomic: TATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGgtcagccatc ... tttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatcatacatgtgcaaagcccatgtcttgctgatctcacataatttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGTAACTGTGTCAAGCGAGTGGTGGTCATTGTGACATCCGTTCTGTTCTTCC
                                  atctcac  putative branch site (score: 3)
 tttctt  putative PPT
 ataatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagccatctaattgattttctaaaaatagcttggccttttgaaatctctggatgcgcttgttcatttcagatagattctatgtgctgaatacattacagttgttacattgatgaatcatcatacatgtgcaaagcccatgtcttgctgatctcacataatttcttgaagGTGTCGTACATGATCCTGGCAAGAGTGTCCCCTGTTACTCACTCGGTGGGTAACTGTGTCAAGCGAGTGGTGGTCATTGTGACATCCGTTCTGTTCTTCC

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