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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaaatgattggcgatctttcgtaaatagttggggggttgcaattactcctacaaatcgatttggtagatgccctttttgcaaatgttaaaaatttcctcttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACTGAGGCATTGGAGAAGAAGATGAG

Basic information

species Oryza sativa
transcript LOC_Os03g25940.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g25940.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G113873_T02 (Zea mays), 3'ss of exon 2
gttagaaatgattggcgatctttcgtaaatagttggggggttgcaattactcctacaaatcgatttggtagatgccctttttgc-----aaatgttaaaaatttcctcttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACTGAGGCATTGGAGAAGAAGATGAG
                             |||| |     | |   || ||| |        |||||   ||||    |||||      |||| ||||   ||  || ||| || |||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||
----------------------------gtagt-gaatattcgtgcttgctcttgt---ctaatttgacggatgtgagttttgacgccgaaatattaagttttatctgttc-cttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG

upper sequence: LOC_Os03g25940.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G075153_T05 (Zea mays), 3'ss of exon 3
gttagaaatgattggcgatctttcgtaaatagttggggggttgcaattactcctacaaatcgatttggtagatgccctttttgcaaatgttaaaaatttcctcttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACTGAGGCATTGGAGAAGAAGATGAG
         | | | |    |  | |    |  ||     | |   || ||| |  |     |||||  ||||  |      | |||| |||||  ||  ||  || || |||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| ||||||||||||||
---------gttcgacatattcccttgtccaaatgaatattcgttcttgctcttgta---taatttgacagat--ctgacgcggaaatattaaattttatctgctc-cttagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGGAACCCGACCACGGAGGCATTAGAGAAGAAGATGAG
















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|29625314|gb|CB630325.1|CB630325
EST:     ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
genomic: ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAGgttagaaatg ... cttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
EST: gi|29645224|gb|CB650231.1|CB650231
EST:     ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
genomic: ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAGgttagaaatg ... cttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
EST: gi|58658021|gb|CK046701.1|CK046701
EST:     CACCGCNGG-CTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
genomic: CACCTC-GGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAGgttagaaatg ... cttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
EST: gi|55411461|gb|CV723837.1|CV723837
EST:     ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
genomic: ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAGgttagaaatg ... cttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
EST: gi|58660550|gb|CK049230.1|CK049230
EST:     GGAGCTCATTGACTTCAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
genomic: GGAGCTCATTGACTTCAAGgttagaaatg ... cttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
EST: gi|58612205|gb|CK039917.1|CK039917
EST:     ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
genomic: ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAGgttagaaatg ... cttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
EST: gi|29614165|gb|CB619178.1|CB619178
EST:     ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
genomic: ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAGgttagaaatg ... cttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
EST: gi|1854173|gb|AA231801.1|AA231801
EST:     CCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
genomic: CCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAGgttagaaatg ... cttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
EST: gi|29660676|gb|CB656951.1|CB656951
EST:     ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAG                         GAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT
genomic: ACACCTCGGCCTACTGGTTCAACAACTCGCAGGAGCTCATTGACTTCAAGgttagaaatg ... cttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcgatttggtagatgccctttttgcaaatgttaaaaatttcctcttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACTGAGGCATTGGAGAAGAAGATGAG
                                       tttcctcttctctc  CT-rich tract
                    tttttgcaaatgttaa  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaaatgattggcgatctttcgtaaatagttggggggttgcaattactcctacaaatcgatttggtagatgccctttttgcaaatgttaaaaatttcctcttctctcagGAGGGGAGGCATGCTAGCTTCGAGTATGGGAGGTATGGTAACCCGACCACTGAGGCATTGGAGAAGAAGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG