Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcttgagccttaaaccatttcctttagctgatttagcagatcccccaattgaagaatagtttctaaggtttatgcctttgcttttatgccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTGCTGAGTCTTCTGCTTTTCTAGCTTATGTTAAGTCAAGCACCCCAACTAC

Basic information

species Oryza sativa
transcript LOC_Os02g40510.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G145058_T01 (Zea mays), 3'ss of exon 4
gtaagtatcttgagccttaaaccatttcctttagctgatttagcagatcccccaat-tgaagaa---tagtttctaaggtttatgcct------ttgcttttat-gccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTGCTGAGTCTTCTGCTTTTCTAGCTTATGTTAAGTCAAGCACCCCAACTAC
|||||    || ||||    ||| ||    |   |||   || | | ||    | | | ||  |   |  |||||     |  |  ||      ||  ||| || || ||| |||||  ||  |  ||||||||| || ||||| |||||| |||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||| | ||
gtaagatgtttcagcc--ggacctttgttctgctctggaatatctggtcttgtattgttaatcacctttatttctctatctattttctgataaattattttaattgcaagCCTCTCCGAGAAGAGCGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTGCCGAGTCGTCTGCATTTCTAGCATATGTCAAGTCAAGCACCCCAGCCAC

upper sequence: LOC_Os02g40510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G365688_T01 (Zea mays), 3'ss of exon 4
gtaagtatcttgagccttaaaccatttcctttagctgatttagcagatcccccaat-tgaagaa---tagtttctaaggtttatgcct------ttgcttttat-gccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTGCTGAGTCTTCTGCTTTTCTAGCTTATGTTAAGTCAAGCACCCCAACTAC
|||||    || ||||    ||| ||    |   |||   || | | ||    | | | ||  |   |  |||||     |  |  ||      ||  ||| || |||||| |||||  ||  | |||||||||| || ||||| |||||| |||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||| | ||
gtaagatgtttcagcc--ggacctttgttctgccctggaatatctggtcttgtattgttaatcacctttatttctctatctgttttctgataaattattttaattgccagCCTCTCCGAGAAGAGTGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTGCCGAGTCGTCTGCATTTCTAGCATATGTCAAGTCAAGCACCCCAGCCAC

upper sequence: LOC_Os02g40510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G174083_T01 (Zea mays), 3'ss of exon 3
gtaagtatcttgagccttaaaccatttcctttagctgatttagcagatcccccaat-tgaagaa---tagtttctaaggtttatgcct------ttgcttttat-gccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTGCTGAGTCTTCTGCTTTTCTAGCTTATGTTAAGTCAAGCACCCCAACTAC
|||||    || ||||    ||| ||    |   |||   || | | ||    | | | ||  |   |  |||||     |  |  ||      ||  ||| || |||||| |||||  ||  |  ||||||||| || ||||| |||||| |||||||||| ||||| ||||| |||||||| ||||| ||||||||||||||| | ||
gtaagatgtttcagcc--ggacctttgttctgccctggaatatctggtcttgtattgttaatcacctttatttctctatctgttttctgataaattattttaattgccagCCTCTCCGAGAAGAGCGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTGCCGAGTCGTCTGCATTTCTAGCATATGTCAAGTCAAGCACCCCAGCCAC

upper sequence: LOC_Os02g40510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G020081_T01 (Zea mays), 3'ss of exon 5
gtaagtatcttgagccttaaaccatttcctttagctgatttagcagatcccccaat-tgaagaa---tagtttctaaggtttatgcct------ttgcttttat-gccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTGCTGAGTCTTCTGCTTTTCTAGCTTATGTTAAGTCAAGCACCCCAACTAC
|||||    || ||||    ||| ||    |   |||   || | ||||    | | | ||  |   |  |||||     |  |  ||      ||  ||| || |||||| |||||  ||  |  ||||||||| || ||||| |||||| |||||||||| ||||| ||||| |||||||| ||||| ||| ||||||||||| | ||
gtaagatgtttcagcc--ggacctttgttctgccctggaatatctgatcttgtattgttaatcacctttatttctctatctgttttctgatcaattattttaattgccagCCTCTCCAAGAAGAGCGTTTTCACGCCCTATAAAAACTAACCTGAGGGTTGCCGAGTCGTCTGCATTTCTAGCATATGTCAAGCCAAGCACCCCAGCCAC

upper sequence: LOC_Os02g40510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G148453_T01 (Zea mays), 3'ss of exon 2
gtaagtatcttgagccttaaaccatttcctttagctgatttagcagatcccccaattgaagaata-gtttctaa--ggtttatgcctttgctttta--tgccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTGCTGAGTCTTCTGCTTTTCTAGCTTATGTTAAGTCAAGCACCCCAACTAC
|||||    || |||||  ||  | |    ||   |  | | |   | || |   ||||    ||  | || |   | ||| ||    |  |||||  |||||||  |||| |||  ||||||||||||||| ||||| |||||| ||| |||||||||||| ||||| |||||||| ||||||||||||||||||||| | ||
gtaagatatttcagcctgtaataactggtcttcctttttgttgttaa-ccacttcttgagttctatatctccatctgttttctgataattattttaattgccagCGACTCCGGGAAGAATGTTTTCACGTCCTATAAAAACTAACCTGAAGGTTGCTGAGTCGTCTGCATTTCTAGCATATGTTAAGTCAAGCACCCCAGCCAC

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|58589830|gb|CF988138.1|CF988138
EST:     AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTT                         CATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGATTG
genomic: AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTTgtaagtatct ... tttatgccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTG
EST: gi|58593163|gb|CF991471.1|CF991471
EST:     AGGCACACCAGAGGGTTTACTAGTCTCCACTGAAGGCGGCGACCAAGCTT                         CATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGATTG
genomic: AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTTgtaagtatct ... tttatgccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTG
EST: gi|29668556|gb|CB664831.1|CB664831
EST:     AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTT                         CATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTG
genomic: AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTTgtaagtatct ... tttatgccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTG
EST: gi|29668596|gb|CB664871.1|CB664871
EST:     AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTT                         CATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTG
genomic: AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTTgtaagtatct ... tttatgccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTG
EST: gi|29640330|gb|CB645339.1|CB645339
EST:     AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTT                         CATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTG
genomic: AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTTgtaagtatct ... tttatgccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTG
EST: gi|29686796|gb|CB683071.1|CB683071
EST:     AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTT                         CATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTG
genomic: AGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTTgtaagtatct ... tttatgccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTG

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: 66 (upstream exon), 62 (downstream exon)
Score: 12

TCTAATCCTTCTGATGCTGAGCCTAAACAAAAAGGCACACCAGAGGGTTTACTAGTCTCTACTGAAGGCGGCGACCAAGCTTgtaagtatct ... tttatgccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTGCTGAGTCTTCTGCTTTTCTAGCTTATGTTAAGTCAAGCACCCCAACTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatcccccaattgaagaatagtttctaaggtttatgcctttgcttttatgccagCATCTCCCGGAGTAATGTTTTCACGTCCAATAAAGACTAACTTGAGGGTTGCTGAGTCTTCTGCTTTTCTAGCTTATGTTAAGTCAAGCACCCCAACTAC
                                     cctttgctttt  CT-rich tract
                 aatagttt  TA-rich tract