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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctacaattctgttgccccagatggcgtacttaaaatctttagattattttattatatttgtttctttctacatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g47220.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 13
gtaagttctacaattctg---ttgccccagatggcgtacttaa-aatctttagattattttattatatttgtttctttctacatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAG
||||||||| || || |    ||  |  ||||||  ||   |   ||| ||   | | || || || |   |||||   |     |||||||||| ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||| || ||||||
gtaagttcttcagttatagtattatcttagatggtatatcaattgatcattgcgtaacttgataatttaaatttctgcatgt-cttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG

upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G178822_T03 (Zea mays), 3'ss of exon 13
gtaagttctacaattctg---ttgccccagatggcgtacttaa-aatctttagattattttattatatttgtttctttctacatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAG
||||||||| ||  | |    ||  |  |||| |  ||   |   ||| ||   ||| || || || |   |||||   ||  || ||||||||| ||||||||||| ||| ||||||||||||||||  ||||||| ||||||||||| ||||| |||
gtaagttcttcagctatagtattatcttagattgtatagcaaccgatcattgcgttacttgataatttaaatttctgcatatctc-gcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCACAGAAGTCCTCCAGCATACCTTCTTCCAG
















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|58595654|gb|CK006182.1|CK006182
EST:     TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCA                         TCACTGTGCTCATGGGACCCTTTCAAGAGACCAAAGGCTGCAGAAGTTCTC
genomic: TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCAgtaagttcta ... acatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTC
EST: gi|58683626|gb|CK072313.1|CK072313
EST:     TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCA                         TCACTGTGCTCATGGGACCCTTTCAAGAGACCAAAGGCTGCAGAAGTTCTC
genomic: TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCAgtaagttcta ... acatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTC
EST: gi|88256807|gb|CI354588.1|CI354588
EST:     TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCA                         TCACTGTGCTCATGGGACCCTTGCAAGAGAC
genomic: TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCAgtaagttcta ... acatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGAC
EST: gi|88664333|gb|CI687436.1|CI687436
EST:     TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCA                         TCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTC
genomic: TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCAgtaagttcta ... acatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTC
EST: gi|58675617|gb|CK064304.1|CK064304
EST:     TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCA                         TCACTGTGCTCATGGGACCCTTTCAAGAGACCAAAGGCTGCAGAAGTTCTC
genomic: TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCAgtaagttcta ... acatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTC
EST: gi|163918501|gb|EG711431.1|EG711431
EST:     TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCA                         TCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTC
genomic: TGGCAGAGGTAATGACATCAGTCAGTAGTGAGGCAGTCGACCTGATTTCAgtaagttcta ... acatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtacttaaaatctttagattattttattatatttgtttctttctacatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAG
                                tttgtttctttctac  CT-rich tract
     ttaaaatctttagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctacaattctgttgccccagatggcgtacttaaaatctttagattattttattatatttgtttctttctacatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT