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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttattctgtaaataattgccagccttttgtcacctcttgcatatttagtttttaagcaaccgagcatgcaaatcattactacactgagttactactgaattattcagtacaaagattgatccttgaaacgcacaaatatcttacctgctgggattgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAGAAGCTGACATCTATAGCCTCCAATTTTATCAGCGACCTCGACAGAATCC

Basic information

species Oryza sativa
transcript LOC_Os03g63710.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 6
-------gtagttat--tctgtaaataattgccagcct--tttgtcacctctt-gcatatttagtttttaagc---aaccgagcatgcaaatcatt---actacactgagttactactga-attattcagt-acaaagattgatccttgaaacgcacaaata-tcttacctgctgggattgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAGAAGCTGACATCTATAGCCTCCAATTTTATCAGCGACCTCGACAGAATCC
       || |  ||   ||||   |  |||  |   |    |||  |  | | |  |   ||  ||||||||   ||  || | |   | | |     |     || ||  |  ||  | |  || |||  ||   |  |||   ||| |       || | ||| |  | |||  || ||| || |||| || || ||||||||||| |||||| | || |||||||| ||||||||||||||||||||| | ||||||||||| ||||||||||| ||||||||||
gtaacttgttggcataacctgttgtttcttggaattttagcgtgtagcaccatagtttgcatacgttttaagccacaattgaac-tatgagttagcggaaacgtgctaaggaaaaaccaataccatgcagagacgtcgtgtgaaagttgcataaagtcaacagtctcatttcctgtcatggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAGAAGCTGACATCTTTCGCCTCCAATTTCATCAGCGACCTGGACAGAATCC

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G176612_T02 (Zea mays), 3'ss of exon 6
gtagttattctgtaaataattgccagccttttgtcacctcttgcatatttagtttttaagcaaccgagcatgcaaatcattactacactgagttactactgaattattcagtacaaagattgatccttgaaacgcacaaatatcttacctg-ctgggattgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAGAAGCTGACATCTATAGCCTCCAATTTTATCAGCGACCTCGACAGAATCC
                                                                                        |    |  |  | || | ||   | |    ||   |   ||   | |    || | | | | | |||  || ||| || |||| || || ||||||||||| |||||| | || || || || ||||||||||||||||||||| | ||||||||||| ||||||||||| ||||| ||||
---------------------------------------------------------------------------------------gtagcctttttgtaaactgttggat-cggcaatc--tttgtggttc-cttggatgtttaagcagtctgccatggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAGAAGCTGACATCTCTGGCCTCCAATTTCATCAGCGACCTGGACAGGATCC

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 6
gtagttattctgtaaataattgccagccttttgtcacctcttgcatatttagtttttaagcaaccgagcatgcaaatcattactacactgagttactactgaattattcagtacaaagattgatccttgaaacgcacaaatatcttacctgctgggattgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAGAAGCTGACATCTATAGCCTCCAATTTTATCAGCGACCTCGACAGAATCC--
                  ||| |   |||| |      | | | |  || | | || | |  |     ||| | ||  || |    |       | || ||    ||| ||| |    ||||||  | |  | | |||  |  ||  |||        |||| ||||||||   || ||||| |||||||| ||||| || || ||||| ||||||||||||||||  ||  | |||||||  || || |  || ||   ||| | |   
----------------gtattccttaccttgtactggatttggaaatttcattattcatgttatttgtcattcgaacaatgaaatgataatcaaattagtgg--catt-agttcctgtattgatgttgg--atgtacacctccctcccct-------ctgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTGAGCTCATTGGCCTCCACATTGATGACAGATCTT--CAGGACCGAA

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|163926732|gb|EG713748.1|EG713748
EST:     CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAG                         GCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
genomic: CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAGgtagttattc ... tgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
EST: gi|38476645|gb|CF960778.1|CF960778
EST:     CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAG                         GCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
genomic: CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAGgtagttattc ... tgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
EST: gi|86592535|gb|CI253216.1|CI253216
EST:     CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAG                         GCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
genomic: CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAGgtagttattc ... tgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
EST: gi|66922735|gb|CX109583.1|CX109583
EST:     CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAG                         GCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
genomic: CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAGgtagttattc ... tgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
EST: gi|29645174|gb|CB650181.1|CB650181
EST:     CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAG                         GCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
genomic: CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAGgtagttattc ... tgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
EST: gi|86497697|gb|CI140330.1|CI140330
EST:     CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAG                         GCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
genomic: CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAGgtagttattc ... tgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
EST: gi|86859205|gb|CI277095.1|CI277095
EST:     CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAG                         GCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
genomic: CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAGgtagttattc ... tgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
EST: gi|88221223|gb|CI221179.1|CI221179
EST:     CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAG                         GCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
genomic: CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAGgtagttattc ... tgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
EST: gi|29677840|gb|CB674115.1|CB674115
EST:     CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAG                         GCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG
genomic: CGAATCTGGATTTAAGTGCTGCGGATCTCATCAACAGAATATCATTCCAGgtagttattc ... tgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagattgatccttgaaacgcacaaatatcttacctgctgggattgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAGAAGCTGACATCTATAGCCTCCAATTTTATCAGCGACCTCGACAGAATCC
                            atcttac  putative branch site (score: 3)
                        aaatatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttattctgtaaataattgccagccttttgtcacctcttgcatatttagtttttaagcaaccgagcatgcaaatcattactacactgagttactactgaattattcagtacaaagattgatccttgaaacgcacaaatatcttacctgctgggattgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAGAAGCTGACATCTATAGCCTCCAATTTTATCAGCGACCTCGACAGAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA