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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttggaattcggttcaatctttgggattgattttgcttgcattgttcgttgatcgctggatgaattgcggatggtttgatttggtctgtttgattttaatttgtttgcacagATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACAAACGCGGCGACTATGTGCCAGGATTGAAG

Basic information

species Oryza sativa
transcript LOC_Os06g13720.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 1
gtgagttggaattcggttcaatctttgg--gattgattttgcttgcattgttc-gttgatcgctggat-----gaattgcggatggtttgatttggtctgtttgattttaatttgtttgcacagATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACAAACGCGGCGACTATGTGCCAGGATTGAAG
|||||||    |         |  ||||     || |  ||||   || || | ||| |||| |||        ||| | |  |||  |  |   ||   ||||   | |  | || |   ||||||||||||||||||| || |||||||| || || ||||| || |||||||| ||||| ||||||||||| || || |||
gtgagttcttctgttaccatgtgcttggtcagctggtagtgctgtgatagtactgttcatcggtgggattccgaaatcgagagtgggctagtggagtgactttggagt-acctggtgtatgcagATGGGATGGGGACGGCAGAGTGGAGGGCCTCCAAGAGCCCGGCTTACTACAAGCGCGGGGACTATGTGCCTGGCTTAAAG
















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|218481294|gb|FG969686.1|FG969686
EST:     GGCGGCGCTCTGGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACT                         ATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
genomic: GGCGGCGCTCTGGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACTgtgagttgga ... gtttgcacagATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
EST: gi|218498886|gb|FG966541.1|FG966541
EST:     GGCGGCGCTCTGGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACT                         ATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
genomic: GGCGGCGCTCTGGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACTgtgagttgga ... gtttgcacagATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
EST: gi|218494727|gb|FG965194.1|FG965194
EST:     GGCGGCGCTCTGGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACT                         ATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
genomic: GGCGGCGCTCTGGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACTgtgagttgga ... gtttgcacagATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
EST: gi|218483908|gb|FG949227.1|FG949227
EST:     GGCGGCGCTCTGGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACT                         ATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
genomic: GGCGGCGCTCTGGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACTgtgagttgga ... gtttgcacagATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
EST: gi|218483530|gb|FG955438.1|FG955438
EST:     GCGGCGCTCTGTGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACT                         ATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
genomic: GCGGCGCTCTG-GAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACTgtgagttgga ... gtttgcacagATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
EST: gi|218494530|gb|FG953442.1|FG953442
EST:     GGCGGCGCTCTGGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACT                         ATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA
genomic: GGCGGCGCTCTGGAAGCTGCCCGTCGTGCTCGTCTGCGAGAACAACCACTgtgagttgga ... gtttgcacagATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatgaattgcggatggtttgatttggtctgtttgattttaatttgtttgcacagATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACAAACGCGGCGACTATGTGCCAGGATTGAAG
                                    ttttaat  putative branch site (score: 3)
                                          tttgttt  CT-rich tract
                               tttgattttaatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttggaattcggttcaatctttgggattgattttgcttgcattgttcgttgatcgctggatgaattgcggatggtttgatttggtctgtttgattttaatttgtttgcacagATGGGATGGGGACGGCGGAATGGAGGGCATCGAAAAGCCCCGCATACTACAAACGCGGCGACTATGTGCCAGGATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG