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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtggttatttgctagctatggatgtgcatgtatacaggatatccgcctgatgtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 45
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 45
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 28
-------------------------------------gtatgtggttatttgctagctatggatgtgcatgtatacaggatatccgcctgatgtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG
                                      |   ||    |      |  |    |     | | |||   || || | |    || |  |  ||||||||||| | || ||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||| |||||||| || |||||||| || ||||||||
gtacatgattgtttgcttgatacatgtttctgaatctcttcatgacattacatctgacacttttcctattctctacgctatttctgacactcgtaatttcttctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTGGGAATGGAAGAAATACGGAGAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 45
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 44
---------------------------------------gtatgtggtta--tttgctagctat--ggatgtgcatg-tatacaggatatccgcctgatgtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG
                                         |||   |||  | ||  |  | |  | |  |   |  | ||||  |  || | |      ||  |  ||||||||||| | || ||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||| |||||||| ||||||||||| || ||||||||
gtacatgactatttgcttgacacatattcctgaacctcttcatgacattacatctgacacttttccgaagctctctactttacactacttctgacactctgcatttcatctttcagGTTCTTCAGAGTACAATATATGAAGTTGACCTTGATCGAATTCTTCAGAGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 45
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 47
---------------------------------gtatgtggttatttgctagctatggatgtgcatgtatacaggatatccgcctgatgtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG
                                  ||| | | ||| |  |    ||  |  |   | | | ||| ||   |   |  | |    |   ||| |||||| | || || || || ||||| ||||||||||||||||| ||||||||||| ||| | ||  |||||||  | || ||||| || ||| |||||||
attgtcaagaagcagagttgaaattgccaaattctatcttgatatgttttgttcattaaaat---tttgttcagtattaacatttatttttttgtg--cttgcagGTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 45
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 48
----------------------------------gtatgtggttatttgctagctatggatgtgcatgtatacaggatatccgcctgatgtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG
                                   | | | | ||| |  ||   ||  |  |   | | | |||  |||   | || | |    ||||  | |||||| | || || || || ||||| ||||||||||||||||| ||||||||||| ||| | ||  |||||||  | || ||||| || ||| |||||||
ctttgtcaagaagcagagttagaattgccaaattctctcttgatatgttttattcattaaaat---tttgttcag--tattaacatg-tatttgtttgtgctgcagGTTCTTCAGAGCACTATCTATGATGTTGACCTTGATCGCATACTTCAAAGCATCCATTTGTACCTGCAAGACTTGGGAATGGAGGAAATTAGGAGAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 45
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 17
---------------------------gtatgtggttatttgctagctatggatgtgcatgtatacaggatatccgcctgat--gtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG
                            ||    || |||  || | |||||   |   ||  ||      |||     |||  |   |    |  | |||||| | |||||||| |||| ||| ||||||||||| ||||| |||||||| || ||| | ||  |||||||| | || |||||||| ||  | |||||
tcaacttgtttgaattatggttgaacattaatatgtcattctcttggtatgggcttctgtgc-tatgatcaatctcatagatcagcttccacatggtgcagGTTCTTCAAAGTACTATATTTGATGTTGACCTTGACCGCATCCTTCAAAGTATACATGTATACCTGCAAGAATTGGGAATGGAAGAAATCAGAAGAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 45
lower sequence: PP1S66_170V6.1 (Physcomitrella patens), 3'ss of exon 46
------------------------------------gtatgtggttatttg-ctagctatggatgtgcatgtatacaggatatccgcctgatgtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG
                                     | |||| || |||  ||  || | |   | | |||     |   |  ||  ||| |     || | |  |||||| |       ||  |   |||||| ||||||||||| |||||||||||||||||    |||||  |||| || || |||| ||| || |||| | |
gtttggaactgattttctcatattctcttgaaattgatttgtgtttctttttctgacttttgtactacgtgtgggttgttaa--cgtgtgaagctgtttt-tatggcagGTTCTTGGTTCAACTTTGCTTGAAGTAGACCTTGATCGAATTCTTCAAAGCATTCACGAGTATTTTGAAGAGCTGGGAATGGCAGAAATACGGAAACG

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|58612256|gb|CK039968.1|CK039968
EST:     ACCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
genomic: ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtatgtggtt ... tgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
EST: gi|300216015|gb|HO088641.1|HO088641
EST:     ACCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
genomic: ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtatgtggtt ... tgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
EST: gi|58673525|gb|CK062211.1|CK062211
EST:     ACCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
genomic: ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtatgtggtt ... tgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
EST: gi|58597274|gb|CK007802.1|CK007802
EST:     ACCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
genomic: ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtatgtggtt ... tgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
EST: gi|88571710|gb|CI663083.1|CI663083
EST:     ATCAGAAGTTCTCACATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
genomic: ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtatgtggtt ... tgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
EST: gi|163921634|gb|EG714160.1|EG714160
EST:     ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
genomic: ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtatgtggtt ... tgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
EST: gi|29680245|gb|CB676520.1|CB676520
EST:     ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
genomic: ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtatgtggtt ... tgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
EST: gi|58667817|gb|CK056503.1|CK056503
EST:     ACCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
genomic: ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtatgtggtt ... tgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
EST: gi|58673773|gb|CK062459.1|CK062459
EST:     ACCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAG                         GTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC
genomic: ATCAGAAGTTCTCAGATTTAGTTGTCAAATGTTTAATTAAGTTGACAAAGgtatgtggtt ... tgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctatggatgtgcatgtatacaggatatccgcctgatgtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG
                               gcctgat  putative branch site (score: 4)
                                            ttgtctttc  putative PPT
              atgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtggttatttgctagctatggatgtgcatgtatacaggatatccgcctgatgtcacattgtctttcagGTTTTACAAAGTACAATATATGAAGTTGACCTTGATCGCATTCTTCAAAGCATTCATATTTATTTGCAAGAACTAGGGATGGAAGAGATTCGGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA