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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC

Basic information

species Oryza sativa
transcript LOC_Os05g04340.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 4
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgt---tctggtggcgattgatgaacccttcatttctt-------------gaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC
||||||   || ||| |||  | |       | || |   || | |    | || | |   |  ||| |  | | ||    |||||   ||||              |||||||||||| |||||||||| || ||||| |||||||| || |||||||| ||||||||||||||||||||||| ||||| |||||||||||||| |||||||| |||||||
gtttgttactatacaaatcagtatgaaactgaattatctggtttttattgtagtatttcacttaggtagtaactaatagctccttcccctctttttttataaaaataaatgatcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAAGACAAGAGATACAAGAATCGTGAGCTGCAAACCATGCGAGTGCTTGACC

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G01220.3 (Glycine max), 3'ss of exon 4
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC
||| | |  | |  | ||  |||||   ||||  | || | ||| |     ||  || | ||  |   |||||||    |||  | | |||  |  | || | ||||| |||||| |||| || || || ||||||||||||||||||||||||||||||||||| || |||||||| ||  ||||||| |||||  |||| || |
gttagccccttg-tatatt-atttagtgtgcatcttttaattgtatggtagtg-atgctttgcagtatattgatgtttactttgtcttttgcctt-tattatgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGGTACAAGAACCGGGAATTGCAAACCATGCGTCTTCTGGATC

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC
        |||| |   |  |||||   ||||  | || | ||| | |||     || | ||  |   |||||||     || ||    |      | |||| ||||| |||||| |||| || || || |||||||||||||||||||||||||||||||||||||| |||||||| || |||||||| |||||  |||| ||||
-------gttagtcccttatatttagtgtgcatcttttaattgtat-aatagtgatgctttgcagaatattgatgttgattttatcctgt---ctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 4
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttct-tgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC
   |||  |      |    |  |  | | ||  ||||  ||| |  |  |  || ||  | |     ||  ||   | | | | | |  ||| |  | ||||  |||| || ||| | || | ||| ||||| ||||| ||||||||||| || |||||||||||||| ||||| || ||||| || |  ||| |  |  | || |
---tgtactgtagtggtgaaacatgggatacatctgttt-gtgggaca-ctcatg-gtgatagaactaatacatattctcatgactgcggtgactcctgttgt-cagGCTAAATGCATTGAGAGCGGGGAGACGGTGGCCATAAAGAAGGTGCTCCAAGACAAGAGATACAAGAATCGAGAGCTCCAGATCATGAGGCTATTGGATC

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 3
gtttgtctttagacagatc-gatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgta--tagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC
   |  ||| |       | ||  |  |    |  ||| || ||||    |    |||     || |   | |  ||     | ||  |  |  | || ||||    |||| || ||| | || | ||| || ||||||||||| |||||||| ||||| ||||||||||| |||||||| || || || |  |||||  | || || |
---taacttcactggagccagacatggggctgatctgtcca-tgtgacgttcaaggtg-----gtagaactaggggatgttctgatcgcgagggtaattttgttgtcagGCAAAATGCATAGAGAGCGGAGAAACTGTGGCTATTAAGAAGGTGCTTCAGGACAAGAGATACAAGAACCGAGAACTTCAGATCATGCGGCTGCTGGAGC

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 4
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC
                                  | ||    ||   ||   |||            | || ||     |||| ||   |    ||     |  ||||||||||| |||||||||| || || |||||||| || ||||| || ||||||||| | || |||||||| ||||| || | ||||||  | || ||||
---------------------------------gtattgctagt-ccaaacagtgcaacaaaagcaggctttatcgtttcttctttctctttggga----atgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGGTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 3
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC
                                        |||||  || | |     | |  |     | |   |||  ||| || ||     | |    |  ||||||||||||| ||||| || ||||| ||||| || ||||||||  | || ||||||||||| || ||||| |||||||||| ||||||  |||||||||
----------------------------------------gtgtgcaaactcg----ctttaatcattctaggctaacgtttc-ttcctgttgggcttcacttcagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCCATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 3
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC
                                        |||||  || | |     | |  |     | |   |||  ||| || ||     | |    | |||||||||||||| ||||| || ||||| |||||||| ||||||||  | || ||||||||||| || ||||| |||||||||| ||||||  |||||||||
----------------------------------------gtgtgcaaactcg----ctttaatcattctaggctaacgtttc-ttcctgttgggcttcactttagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCTATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 4
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC
                          ||    || || ||    ||  |          | ||     || | |    | |||  ||   |||||         ||||||||||| |||||||||| || || |||||||| || ||||| || ||||||||| | || |||||||| ||||| || | ||||||  | || ||||
--------------------------gtattgctagtccaaacagtgca---acaaaagcaggcttttatcgtttcttctttctctttgggaatg--------cagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGCTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

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|12622374|gb|AU172587.1|AU172587
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|29628929|gb|CB633940.1|CB633940
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAT
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|88298568|gb|CI563563.1|CI563563
EST:     CATGGCCGAGCCGTGTCGTANGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGGAGACTGGTGGCTATAAAGAAGGTTCTTT
genomic: CATGGCCGAGC-GTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTG-AGACTG-TGGCTATAAAGAAGGTTCTT-
EST: gi|58601571|gb|CK012099.1|CK012099
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGC
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGC
EST: gi|58663289|gb|CK051975.1|CK051975
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|33658344|gb|CF280957.1|CF280957
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|29630931|gb|CB635940.1|CB635940
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|58603162|gb|CK013690.1|CK013690
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|29626488|gb|CB631499.1|CB631499
EST:     CATGGGCC-AGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: CATGG-CCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|29629558|gb|CB634567.1|CB634567
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|25798115|gb|CA754076.1|CA754076
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|58598716|gb|CK009244.1|CK009244
EST:     ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAG                         GCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ACATGGCCGAGCGTGTCGTAGGTCATGGATCCTTTGGAACTGTTTTCCAGgtttgtcttt ... tcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC
                gattgat  putative branch site (score: 4)
                             ttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC