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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtctttggtcaacatcagattcatccccagtgttttggcttgccattaatttttccattgtgagctctgtttatcaatctgacctgcctttttgctccttctcag

Basic information

species Oryza sativa
transcript LOC_Os04g41100.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G179097_T04 (Zea mays), 5'ss of exon 2
ATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtctttggtcaacatcagattcatccccagtgttttggcttgccattaa--tttttccattgtgagctctgttta-tcaatct---gacctgccttt-ttgctccttctcag-----
|||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||  |||||||||| |||||| ||||||||||||||||||||||||||||| | || ||||||||||| | ||  ||||||||||| || |   |||  || |||  ||| ||| |||||||  ||||      |||   | ||| ||||||||| |        
ATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGAAGCCCATTAAAACCTTATACTCAACTGGTTGTGACTTTGTGGTACAGgtaggtcatcggacaacatcagatcc-tcagcagtgttttggttttcttctaaagttattcagttgagagttctgtttggtcaaatcaaggactcacttttcttgctccttgtggctacag

upper sequence: LOC_Os04g41100.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 2
ATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtctttggtcaacatcagattcatccccagtgttttggcttgccattaa--tttttccattgtgagctctgttta-tcaatct--gacctgccttt-ttgctccttctcag-----
|||||||||||||||| |||||||||||||||||||| |||||||||||||| |||||  |||||||||| |||||| ||||||||||||||||||||||||||||| | || ||||||||||||| ||  ||||||||||| || |   |||  || |||  ||| ||| |||||||  |||| |   |||   ||||| ||||||||| |        
ATAACCGTGGTGAGTTAAAAATATGTGATTTTGGACTGTCTCGTCAATATGGGAGCCCATTAAAACCTTATACTCAACTGGTTGTGACTTTGTGGTACAGgtaggtcatcggacaacatcagattcctcagcagtgttttggttttcttctaaagttattcagttgagagttctgtttggtcaaccaaggactcacctttcttgctccttgtggctacag

upper sequence: LOC_Os04g41100.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G179097_T07 (Zea mays), 5'ss of exon 2
-----------------------------ATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtctttggtcaacatcagattcatccccagtgttttggcttgccattaatttttccattgtgagctctgtttatcaatctgacctgcctttttgctccttctcag
                             |||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||  |||||||||| |||||| ||||||||||||||||||||||||||||| |                                                                                                    
GGATCTGAAGACCTCAAATCTTTTGTTGAATAACCGTGgtgagttaaaaatatgtgattttggactgtctcgtcaatatggaagcccattaaaaccttatactcaactggttgtgactttgtggtacaggtaggtcat----------------------------------------------------------------------------------------------------

upper sequence: LOC_Os04g41100.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA18G01230.1 (Glycine max), 5'ss of exon 3
ATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtc-tttggtca-acatcagattcatccccagtgttttggcttgccattaatttttccat-tgtgagctctgtttatcaatctgacctgcctttttgctccttctcag
||||  | |||||||| ||||| |||||||||||| |  ||||||||||||| |||||  | ||||| || || ||  |||| || ||| | ||||||||||  ||| |||||||| ||||   |||  |  |   |||||   | || || |  ||  |   | ||  |   ||  ||||   ||     |    || ||           
ATAATAGGGGTGAGTTAAAAATTTGTGATTTTGGATTGGCTCGTCAATATGGGAGCCCATTGAAACCATATACACACCTGGTGGTTACTCTTTGGTACAGgtgagtcatttggtcagacatgccatttttttc---tgtttattcatgtcactggttaatttgtatgatattcctcattatagttcaattttattgttgtgaa---------

upper sequence: LOC_Os04g41100.4 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G67580.1 (Arabidopsis thaliana), 5'ss of exon 1
ATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtctttggtcaacatcagattcatccccagtgtt-ttggcttgccattaatttttccattgtgagctctgtttatcaatctgacctgcctttttgctccttctcag
| || || ||||||||||| |||||||| |||||  |  |||| |||||||| |||||||| || ||||| |||||  ||||||| ||  | |||||||||||         |  ||   |   |  |    |      ||   | |   |||  ||| | |||||      | |||   | ||||     | || ||| |  || |   
ACAATCGGGGTGAGTTGAAGATATGTGACTTTGGTTTGGCTCGGCAATATGGCAGCCCGCTCAAGCCTTATACTCATCTGGTTGTTACGCTTTGGTACAGgtaaagtgcgtttttaccctattcttgtttataaaaaaattaagtggtgtttacatttacgattgt------tatttga-attctggtggactttcttgtttttttt---

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|218494622|gb|FG958132.1|FG958132
EST:     CGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCA-AACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: CGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|58691737|gb|CK080424.1|CK080424
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|29640024|gb|CB645033.1|CB645033
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|58587583|gb|CF985891.1|CF985891
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTA
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTA
EST: gi|33678455|gb|CF306694.1|CF306694
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGCGGTACAG                         GGCGCCAGAACTATTATTATGAACGAAAGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|163929543|gb|EG709310.1|EG709310
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|58686625|gb|CK075312.1|CK075312
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|58687429|gb|CK076116.1|CK076116
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
EST: gi|29679248|gb|CB675523.1|CB675523
EST:     GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAG                         GGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT
genomic: GGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATAT

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: 71 (upstream exon), 62 (downstream exon)
Score: 28

ATAACCGTGGTGAGTTGAAAATATGTGATTTTGGACTATCTCGTCAATATGGAAGCCCGCTAAAACCTTACACTCAATTGGTTGTGACTTTGTGGTACAGgtaggtcttt ... tccttctcagGGCGCCAGAACTATTATTAGGAACGAAGGAATATTCTACCGCCATTGATATGTGGTCTGTGGGCTGCATAATGGCAGAGCTTTTGGCCAAAGAACCATTA




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