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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccataagttttaacctgatgtggaatacttgtttcagttcttttcgtagctgctgttcaccttcacaatttctgcagacttcagagtgctatatgcttctattttatgtgtaacaagtacttttatgggcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA

Basic information

species Oryza sativa
transcript LOC_Os07g12830.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12830.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G167946_T01 (Zea mays), 3'ss of exon 1
gtaaccataagttttaacctgatgtggaatacttgtttcagttcttttcgtagctgctgttcacct-tcacaatttctgcagacttcagagtgctata-tgcttctattttatgtgtaacaagtacttttatgggcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
|||| | || |||| ||  |  |  |   |  |  |||       ||||  | |  |||||| | | |||||| |     |   ||    ||  |||  | | | |   | |  || | ||  |   |||  |   ||||||||| ||||||||||||||||| || ||||| ||||||   ||  |  ||||||
gtaatctta-gtttcaatttattcagacttgttctttttgag---tttcagaaccactgttctcatctcacaagtggca-acctttttctgtattatggtacattttcctaacctgaatcatat---tttgggttgatttgcagGTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACC--ACTACATTGTTCA

upper sequence: LOC_Os07g12830.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152438_T02 (Zea mays), 3'ss of exon 5
gtaaccataagttttaacctgatgtggaatacttgtttcagttcttttcgtagctgctgttcaccttcacaatttctgcagacttcagagtgctatatgcttctattttatgtgtaacaagtacttttatgggcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
                         | ||   | |||||||||| || |  || ||    | |  |||| ||      |||  |||  | |   | | |   | |  || | |||| || |            |||||||||| ||||||||||||||||| || ||||| |||||||  || ||| ||||||
-------------------------gtaaccatagtttcagttcatt-cagagttg----ttagtttcagaac-----cagtgttctca-tctcacaaggcacaaccttttctgtatcatg---------atacatttgcagGTGTTGATATGCTTATGAAAGCCGCTGGGAAAGACTGCACTGCTTTGTTCA
















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|86252073|gb|CI055810.1|CI055810
EST:     GAAAGGTCGTGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAG                         GAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
genomic: GAAAGGTCGTGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAGgtaaccataa ... gcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
EST: gi|33680256|gb|CF308495.1|CF308495
EST:     GAAAGGTCGTGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAG                         GGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTC
genomic: GAAAGGTCGTGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAGgtaaccataa ... gcatttgcagG-AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTC
EST: gi|88491319|gb|CI428591.1|CI428591
EST:     CAACATTGCTCCGTACATGAAATTTCATCCGGGAG                         GAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
genomic: CAACATTGCTCCGTACATGAAATTTCATCCGGGAGgtaaccataa ... gcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
EST: gi|86420762|gb|CI056751.1|CI056751
EST:     GAAAGGTCGTGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAG                         GAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
genomic: GAAAGGTCGTGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAGgtaaccataa ... gcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
EST: gi|3762892|gb|AU029644.1|AU029644
EST:     GAAAGGTCGTGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAG                         GAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
genomic: GAAAGGTCGTGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAGgtaaccataa ... gcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
EST: gi|88990983|gb|CI108370.1|CI108370
EST:     GAAAGGTCGTGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAG                         GAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
genomic: GAAAGGTCGTGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAGgtaaccataa ... gcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
EST: gi|88831337|gb|CI082147.1|CI082147
EST:     TGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAG                         GAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
genomic: TGTGTACAACATTGCTCCGTACATGAAATTTCATCCGGGAGgtaaccataa ... gcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgctatatgcttctattttatgtgtaacaagtacttttatgggcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA
                        gtgtaac  putative branch site (score: 3)
                tattttatgtgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccataagttttaacctgatgtggaatacttgtttcagttcttttcgtagctgctgttcaccttcacaatttctgcagacttcagagtgctatatgcttctattttatgtgtaacaagtacttttatgggcatttgcagGAGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA