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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaattctgtcagttgataatttcgtatgtatttctctaccttgttactacgaaatctcagtggaatttcagttagcattatcaaacacataggattggtcatactctagactgcaagagcttttacgtgctgcctgctcttgtggagtactgtggatcgctgacgaatttatttttgtttcttcagGGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAAAAGTTTTTGACAGAAGAGGCCATGTTGCAAAACTCTGCATTATTATTCT

Basic information

species Oryza sativa
transcript LOC_Os01g49820.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 5
gtaagtgaattctgtcagttgataatttcgtatgtatttctctaccttgttactacgaaatctcagtggaatttcagttagcattatcaaacacataggattggtcatactctagactgcaagagcttttacgtgctgcctgctcttgtggagtactgtggatcgctgacgaatttatttttgtttcttcagGGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAAAAGTTTTTGACAGAAGAGGCCATGTTGCAAAACTCTGCATTATTATTCT
                                                                             || | |  |  ||     ||   ||      | |||||| |  ||    ||  |   ||||       | ||||| ||||           | || ||||| ||| | |    ||||||||||||||||||||| ||||| ||||||||| ||||||||||||| ||||| || ||  | ||||| |||||||||||| |||||||| |  ||  
-----------------------------------------------------------------------------ttcgtagcacaaagt---tattgttctcttgagtctagaatataaacttttcaatcagctgttactgttggtggattact---------caaagattttatgtttatctt---agGGTCTTTTGCTGGCCTTGGGTTCCTTTCATGGTATTTGGCTGGTAAAATCAAAGTATTCGATCGTAGAGGACATGTTGCAAAAGTCTGCATTGTCCTTTC

upper sequence: LOC_Os01g49820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G06580.1 (Glycine max), 3'ss of exon 4
gtaagtgaattctgtcagttgataatttcgtatgtatttctctaccttgttactacgaaatctcagtggaatttcagttagcattatcaaacacataggattggtcatactctagactgcaagagcttttacgtgctgcctgctcttgtggagtactgtggatcgctgacgaatttatttttgtttcttcagGGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAAAAGTTTTTGACAGAAGAGGCCATGTTGCAAAACTCTGCATTATTATTCT
                             ||| ||| |    || || ||| | |  ||||    ||    | |   | |     | | |    | | | ||| ||  ||  |  |||   | |  | | |  ||  |  ||   ||   |  |  | |   | | | |  |||  ||           ||||||| |||||||| ||||||||||| ||||||||  |  | || ||| | | ||| |||||  | || || ||| |||  ||||| ||| |  |  | ||
-----------------------------gtaagtagtagaatatct-gtttcaa--aaataatggttaggtgttgatgacatgaacctagtctagaaggttg-tctaaccattaactatgaaaattatcaattgtggaatgtgttt---ggcttttttaatttggtaattaataaatg----------cagGGTCCTTTGCTGGTCTTGGTTTCCTTTCATGGTACTTATCAGGGAAAGTTAGAGTGTTTGATCGCAGGGGGCATATTGGGAAACTATGCCTAGTCTTGCT

upper sequence: LOC_Os01g49820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G29390.1 (Glycine max), 3'ss of exon 6
gtaagtgaattctgtcagttgataatttcgtatgtatttctctaccttgttactacgaaatctcagtggaatttcagttagcattatcaaacacataggattggtcatactctagactgcaagagcttttacgtgctgcctgctcttgtggagtactgtggatcgctgacgaatttatttttgtttcttcagGGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAAAAGTTTTTGACAGAAGAGGCCATGTTGCAAAACTCTGCATTATTATTCT
                                                                                 | | |||  |  | |     | |||  ||  | || |   | |  | | |  ||  |  ||   ||      |  | |   | | | |  |||  ||           ||||||| |||||||||||||||||||| ||||||||  |  |  | ||| | | ||| |||||  | || ||| || |||  ||||| ||| |  |  | ||
----------------------------------------------------------------------------acggtcctaatcccagtcttgaaggttgtctaaccattgaatatgaaaattatcaattgtggtatgtgttt------ttttttaatttggtaattaataaatg----------cagGGTCCTTTGCTGGCCTTGGTTTCCTTTCATGGTACTTATCAAGGAAAGTTAGAGTGTTTGATCGTAGGGGCAATATTGGGAAACTATGCCTAGTCTTGCT

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|27547046|gb|CA765107.2|CA765107
EST:     GAGCGTTATCAAAGGAGGTCACAAGAGTTTTCCGAGTGGCCATACTTCTT                         GGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAA
genomic: GAGCGTTATCAAAGAAGGTCACAAGAGTTTTCCGAGTGGCCATACTTCTTgtaagtgaat ... gtttcttcagGGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAA
EST: gi|25807069|gb|CA763030.1|CA763030
EST:     AAAGAAGGTCACAAGAGTTTTCCGAGTGGCCATACTTCTT                         GGTCTTTNGCTGGCCTGGGTTCCCGGTCATGGTATCTGGCTGGTAAAATAA
genomic: AAAGAAGGTCACAAGAGTTTTCCGAGTGGCCATACTTCTTgtaagtgaat ... gtttcttcagGGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAA
EST: gi|5771042|gb|AU077931.1|AU077931
EST:     GAGCGTTATCAAAGAAGNTCACAAGAGTTTTCCGAGTGNCCATACTTCTT                         GGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAA
genomic: GAGCGTTATCAAAGAAGGTCACAAGAGTTTTCCGAGTGGCCATACTTCTTgtaagtgaat ... gtttcttcagGGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgctcttgtggagtactgtggatcgctgacgaatttatttttgtttcttcagGGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAAAAGTTTTTGACAGAAGAGGCCATGTTGCAAAACTCTGCATTATTATTCT
                          cgctgac  putative branch site (score: 3)
                                    tttatttttgtttctt  putative PPT
                                  aatttatttttgtttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaattctgtcagttgataatttcgtatgtatttctctaccttgttactacgaaatctcagtggaatttcagttagcattatcaaacacataggattggtcatactctagactgcaagagcttttacgtgctgcctgctcttgtggagtactgtggatcgctgacgaatttatttttgtttcttcagGGTCTTTTGCTGGCCTTGGTTTCCTGTCATGGTATCTGGCTGGTAAAATAAAAGTTTTTGACAGAAGAGGCCATGTTGCAAAACTCTGCATTATTATTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG