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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_Os04g41100.4
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