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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctttcttcagcttattttgttgattatcgtggatcttgcattgtgcttgaccgataagatggactaattcacatttagaccatagttgtacat...

Basic information

species Oryza sativa
transcript LOC_Os03g18510.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18510.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G058138_T01 (Zea mays), 5'ss of exon 3
CATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctttcttca-gcttattttgt-tgattatcgtggatcttgcattgtgcttgaccgataagatggactaattcacatttag-accatagttgtacat
 |||| ||| ||||||||||| || |||||||||||||| ||||||||||| |||||||| |||||||||||||| ||||||||||| || ||||||||||| |    | | ||    |||| | | | |||  |   ||       |       ||||    |    ||  || |  | |||||   | || |  |||    
TATGAAGAAAGCTGAAGCTGCGGGCAATGATAATTGTCCTGTGAAGATTAAACTAGTTGCTCCTCCACTTTATGTTCTGACCACACAGACCCTTGACAAGgttgacattattttagtacttaatatatgtgagcaatttgttatagccgagccttttgaagttttgtctgccctgaggcccatttctcatcaaatctgtg---

upper sequence: LOC_Os03g18510.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G083262_T02 (Zea mays), 5'ss of exon 3
CATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctttcttcagcttattttgttgattatcgtggatcttgcattgtgcttgaccgataagatgga--ctaattcacatttagaccatagttgtacat--
 |||| ||| ||||||||||| || |||||||| ||||| |||||||||||||||||||| ||||||||||||||  |||||||||| || ||||||||||| ||   | |||| ||      ||  | ||    |||     |   || |    ||   ||  |||  |   | ||      | |  ||     |   ||   
TATGAAGAAAGCTGAAGCTGCGGGCAATGATAACTGTCCTGTGAAGATTAAGCTAGTTGCTCCTCCACTTTATGTTTTGACCACACAGACCCTTGACAAGgttggcattatctt-agt---acttaataatatgtgtgagcaatttgttatagccgagttatttgataaagtttcatatgtgctcaagcccattctcctcaaat

upper sequence: LOC_Os03g18510.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv13s0067g01710.t01 (Vitis vinifera), 5'ss of exon 5
CATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctttcttcagcttattttgttgattatcgtggatcttgcattgtgcttgaccgataagatggactaattcacatttagaccatag-ttgtacat
 ||| |||| || ||||| || || ||| |  ||||||||||||| ||||| || ||||| ||||| |||||||| || || || || || |||||||||||     |    |  |||  |   | ||     | |   || ||      ||  |     |        |||  ||  |   |      | | ||| |   
AATGCGGAAAGCAGAAGCGGCGGGCAATAAGGATTGTCCAGTGAAAATTAAACTGGTTGCTCCTCCGCTTTATGTTCTTACTACTCAGACGCTTGACAAGgtaatgacacagtgtagcaaacaat-ttccccctggataattttattgcctgtgtttagtacggagcaaacttgtttcctcctttttggtgggttgaatgg

upper sequence: LOC_Os03g18510.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S55_319V6.1 (Physcomitrella patens), 5'ss of exon 6
CATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctttcttcagcttattttgttgattatcgtggatcttgcattgtgcttgaccgataagat--ggactaattcacatttagaccatagttgtacat-----------------------------------------------------------------------------
 ||||| ||||| || |||||||| | |||  | ||||| |||||||||||| |||| ||||| |||||||||||| | |||||||| || |||||||||||  ||    ||| ||   |||||||| |   ||    ||| ||  |    | ||||   |||        ||  ||   ||| ||      || | |||||                                                                             
AATGAGAAAGGCAGAGGCTGCTGGAACTGAAGAGTGTCCTGTGAAGATTAAGTTAGTGGCACCCCCACTTTATGTGATCACCACACAGACACTTGACAAGgtgagttaaatctaca---tattttgtggg--atttaagattttaaacca-ggttgataaatacatcccaaacagatgttcatatattggtcagct-tacatcgaataaacatgaaatgctaccgttttagtttttactattttcaaagctcgtattcaacttgtgcattgcttgtcag

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|89181133|gb|CI045216.1|CI045216
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|88221904|gb|CI221860.1|CI221860
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|87028029|gb|CI257189.1|CI257189
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACCGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|29615907|gb|CB620919.1|CB620919
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|86254774|gb|CI061085.1|CI061085
EST:     TGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: TGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|86495831|gb|CI138464.1|CI138464
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|88216977|gb|CI216681.1|CI216681
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|86498995|gb|CI141628.1|CI141628
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|86538554|gb|CI178760.1|CI178760
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|86888073|gb|CI297890.1|CI297890
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|88991140|gb|CI108527.1|CI108527
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|3767755|gb|AU031782.1|AU031782
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|88202270|gb|CI202625.1|CI202625
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|4714850|gb|AU055967.1|AU055967
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|88960582|gb|CI006543.1|CI006543
EST:     TGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: TGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|86537961|gb|CI178167.1|CI178167
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|89176760|gb|CI013333.1|CI013333
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|88986674|gb|CI033817.1|CI033817
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCCATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|29615906|gb|CB620918.1|CB620918
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|86502170|gb|CI144803.1|CI144803
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|88831641|gb|CI369323.1|CI369323
EST:     CTGACCACACAAACTCTTGACAA-                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: CTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|86413314|gb|CI067719.1|CI067719
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|86537698|gb|CI177904.1|CI177904
EST:     AGCTAGTTGCACCTCCACTTTATGAGCTGACCCCACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACATCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|29615940|gb|CB620952.1|CB620952
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|86412816|gb|CI067221.1|CI067221
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|87018064|gb|CI275878.1|CI275878
EST:     AGCTAGTTGCACCTCCACGTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
EST: gi|218497968|gb|FG969492.1|FG969492
EST:     AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAG                         GACCAACGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG
genomic: AGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 75 (downstream exon)
Score: 26

CATGAGGAAGGCTGAAGCTGCTGGTAATGATAATTGTCCAGTGAAGATTAAGCTAGTTGCACCTCCACTTTATGTGCTGACCACACAAACTCTTGACAAGgtcggtgctt ... tcttgaacagGACCAAGGCATTTCAGTTCTCACTGATGCAATTAAAGCTTGCACAGCTGAGATCGAGAAGCACAAGGGAAAGTTGATAGTTAAGGAAGCACCGAGAGCT




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