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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgcttattctacctttttataagttttgttaaaaggagcaattgtttcacatttgacaaatggaaacaattgatgtgtccaaacatgtggcac...

Basic information

species Oryza sativa
transcript LOC_Os01g16190.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16190.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G467059_T03 (Zea mays), 5'ss of exon 3
ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgcttattctacctttttataagt--tttgttaaaaggagcaattgtttcacatttgacaaatggaaacaattgatgtgtccaaacatgtggcac-
 ||||||||||| || |||||||||||||| |||||||| || || || ||||| ||||| ||||||||||| |||||||||||   ||     | || || | |||| |||      ||  |    |  |         |  |||    |  | |  |  ||   ||||   | |  |      
GCCAGAAATGGTTGTAGGCTGGTATCACTCACATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttaca---aatccacttgtttaaaagggaccggtctatgaaaataggatagcttctgttgttgcactgtactatatgtcatgtcattataaatactgat

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G033626_T01 (Zea mays), 5'ss of exon 3
ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgcttattctacctttttataagttttgttaaaaggagcaattgtttcacatttgacaaatggaaacaattgatgtgtccaaacatgtggcac----
 ||||||||||| || || ||||||||||| |||||||| || ||||| ||||| ||||| || |||||||| |||||||||||  ||     |   ||   | | || |||   | ||    |||    |   |  | |   || |  ||    || |||   ||| | |  ||||         
GCCAGAAATGGTTGTAGGTTGGTATCACTCACATCCTGGCTTCGGATGCTGGCTATCAGGCGTCGATATCAATACTCAGCAGgtctatgcaaatccacttgttctctaaaagggatctttt--ggaatggtctatcaaaacaggatagctgctgtca-ttgcactgtacta-tatgtcatgtcaac

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EDP09161 (Chlamydomonas reinhardtii), 5'ss of exon 4
ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgcttattctacctttttataagttttgttaaaaggagcaattgtttcacatttgacaaatggaaacaattgatgtgtccaaacatgtggcac-------
 || || ||||||||||||||||| ||||| || || || || || || ||||| ||||| || ||||||||||| |||||||||  |   | |       | |     | |  | | | || |  |||| | |  |     |  |     |    |  ||  | | |   |||   ||||        
CCCGGAGATGGTGGTGGGCTGGTACCACTCACACCCCGGCTTCGGCTGCTGGCTGTCAGGCGTGGATATCAACACGCAGCAGgtgtgttgtcgtgcgggggcgt---gcaggaatcgctcaa-gccgcaagtctccc---cgtagcgtgcagcgtaagctggcggggcgcgacaccaggcaaccgcacg

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S181_105V6.1 (Physcomitrella patens), 5'ss of exon 4
ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcat-atgcttattctacctttttataagttttgttaaaaggagcaattgtttcacatttgaca-aatggaaacaattgatgtg----tccaaacatgtggcac------------------------------------------------------------
 ||||||||||| |||||||||||||| || ||||| || ||||| || ||| | || ||||| ||||| || ||||| |||||   | | ||||   ||| ||||   |   ||  |||    |   | | |||   ||  | || | |||   |  |  | | |      |||| |  || |  ||                                                            
GCCAGAAATGGTTGTGGGCTGGTATCATTCACATCCAGGTTTTGGTTGCTGGTTATCTGGTGTGGATATAAATACTCAACAGgtaagttaggcttgcactaactttcgttc--ttgcgttttgggtcccgaatgtgcaacggtggaaacaataccatgatctaacgcagtcttccatagttgggagaccggtatccccctccagaatcactgccagtgttctaaagcagtatccttgtgtatttgcag

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtg-catatgcttattctacctttttataagttttgttaaaaggagcaattgttt-cacatttgacaaatggaaacaattgatgtgtccaaacatgtggcac-
|||||| ||||||||||||||||| || || ||||| || ||||| || ||| | || || || |||||||| |||||||||||    || | ||||  |    |||   |  ||||  | ||||  |   || |   |||||   | | |||     ||   || ||    ||| | |||    
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttaggtttataattaggtttggcatctttttgttaaagtggttgttatgaacacatacaa-agatgtggtgaacaaat-tggtggaacgt-tggtttt

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ16494 (Selaginella moellendorffii), 5'ss of exon 3
ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgt--gcatatgcttattctacctttttataagttttgttaaaaggagcaattgt---ttcacatttgacaaatggaaacaattgatgtgtccaaacatgtggcac
| | |||||||| || || |||||||| || ||||||||||| || || |||||||| || ||||||||||| ||||| ||||   | | |      |     |||| | | | ||| | |  |     ||  | |   ||   | |||||   || |                             
ATCGGAAATGGTTGTAGGATGGTATCATTCACATCCTGGATTCGGGTGCTGGCTTTCTGGAGTTGATATCAATACTCAACAGgcaaggagaaaaaagtctagtctttgtttcactttggatggagttcacagatatgttttggaacttgacttgtgcag----------------------------

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|33684434|gb|CF312673.1|CF312673
EST:     CAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: CAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|55908865|gb|AU032022.2|AU032022
EST:     TCCTGGATTTGGATGTTGGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: TCCTGGATTTGGATGTTGG-CTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|38480043|gb|CF964132.1|CF964132
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGCGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|6552253|gb|AU082081.1|AU082081
EST:     GGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTTNAATCCCAGGNCTGTTGCAGTTGTGATAGACCCAAT
genomic: GGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGC-TTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAAT
EST: gi|58678825|gb|CK067512.1|CK067512
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|38476931|gb|CF961064.1|CF961064
EST:     ATCCTGNATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGTGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|38478871|gb|CF963004.1|CF963004
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|58691729|gb|CK080416.1|CK080416
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|58598852|gb|CK009380.1|CK009380
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|88290588|gb|CI666961.1|CI666961
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|58679699|gb|CK068386.1|CK068386
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|6552265|gb|AU082093.1|AU082093
EST:     TCCTGGATTTTGGATGTTTGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTTAAGCTTTAAATCCCA
genomic: TCCTGGATTT-GGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCA
EST: gi|86872923|gb|CI326920.1|CI326920
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|58675840|gb|CK064527.1|CK064527
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|58682525|gb|CK071212.1|CK071212
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGACTGTTGCAGTTGTGATAGACCCAAT
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGG-CTGTTGCAGTTGTGATAGACCCAAT
EST: gi|58659705|gb|CK048385.1|CK048385
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCTAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|66926046|gb|CX112894.1|CX112894
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|58677541|gb|CK066228.1|CK066228
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|218502937|gb|FG945477.1|FG945477
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAG
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAG
EST: gi|27548512|gb|CA767507.2|CA767507
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|58597372|gb|CK007900.1|CK007900
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|58677827|gb|CK066514.1|CK066514
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|572299|gb|D41810.1|D41810
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTAATAGACC-AATT
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATC
EST: gi|58675425|gb|CK064112.1|CK064112
EST:     ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAG                         AGTTTCGAAGCTTTAAATCCCAGGGGCTGTTGCAGTTGTGATAGACCCAAT
genomic: ATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGG-CTGTTGCAGTTGTGATAGACCCAAT

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: 74 (upstream exon), 73 (downstream exon)
Score: 53

ACCAGAAATGGTGGTGGGCTGGTATCACTCCCATCCTGGATTTGGATGTTGGCTTTCAGGTGTTGATATCAACACTCAGCAGgtgcatatgc ... aattgtgcagAGTTTTGAAGCTTTAAATCCCAGGGCTGTTGCAGTTGTGATAGACCCAATCCAGAGTGTCAAGGGGAAGGTGGTCATTGATGCATTTCGTCTCATTAATC




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