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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCACTCAAAGAAGGAATGGGAGGAGGCAGCAGCAGTGATTTCCATAGTCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaattatgaaaaatgctttactttgatcctttatccttctatattttagaatgaaatatgcacctatttactgttttgtggttgaaagtag

Basic information

species Oryza sativa
transcript LOC_Os02g43930.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43930.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G118731_T01 (Zea mays), 5'ss of exon 3
GATGCACTCAAAGAAGGAATGGGAGGAGGCAGCAGCAGTGATTTCCATAGTCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaattat---gaaaaatgctttactttgatcctttatcctt-ctatattttagaatgaaata-tgcacc---tatttactgttttgtggttgaaagtag
||||| || || |||||||||||||||||||||||||||||||||||||| || |||||  | ||||||||| |||||| |  |  | |   ||||||||||||| ||| |||   |     |  ||||  |  ||| ||  | | | ||    ||| || | ||||| | |||    ||||||  | ||| ||||| | ||   
GATGCCCTTAAGGAAGGAATGGGAGGAGGCAGCAGCAGTGATTTCCATAGCCCTTTCGACATTTTTGAGCAACTTTTTCCGGGTTCTAGCACCTTTGGGGgtaatcaaaatatcttgtggtgttgtttatatatatcgttgcttcatgcttccctttggattaaaatactacactggttatttatcggtttatggttaatag---
















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|29673001|gb|CB669276.1|CB669276
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|218492553|gb|FG956401.1|FG956401
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58661241|gb|CK049921.1|CK049921
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58677822|gb|CK066509.1|CK066509
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58666150|gb|CK054836.1|CK054836
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58601753|gb|CK012281.1|CK012281
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|27577056|gb|CA999750.1|CA999750
EST:     ATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: ATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58601372|gb|CK011900.1|CK011900
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58658625|gb|CK047305.1|CK047305
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58663897|gb|CK052583.1|CK052583
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|33797209|gb|CF324468.1|CF324468
EST:     TATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58672684|gb|CK061370.1|CK061370
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|29627563|gb|CB632574.1|CB632574
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|218489299|gb|FG965759.1|FG965759
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58695486|gb|CK084173.1|CK084173
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58664824|gb|CK053510.1|CK053510
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAAGCGTGGCGAAGATGTGGTACATACTATGAAG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAA-GCGTGGCGAAGATGTGGTACATACTATGAAG
EST: gi|29619928|gb|CB624940.1|CB624940
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|13420811|gb|AU174901.1|AU174901
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|33796281|gb|CF324007.1|CF324007
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|33795773|gb|CF323756.1|CF323756
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         T
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtag-
EST: gi|33795773|gb|CF323756.1|CF323756
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         T
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtag-
EST: gi|33795773|gb|CF323756.1|CF323756
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         T
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtag-
EST: gi|27576325|gb|CA999019.1|CA999019
EST:     ATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: ATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|58687630|gb|CK076317.1|CK076317
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|29683463|gb|CB679738.1|CB679738
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGG
EST: gi|29631437|gb|CB636446.1|CB636446
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         GTAGAGGACACAGACAAAAGCGTGGCG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... ttgaaagtagGTAGAGGACACAGACAAAAGCGTGGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCACTCAAAGAAGGAATGGGAGGAGGCAGCAGCAGTGATTTCCATAGTCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaattatgaaaaatgctttactttgatcctttatccttctatattttagaatgaaatatgcacctatttactgttttgtggttgaaagtag

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