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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 19
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag
|||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||| | ||| || || | ||| | ||| || | | ||||| ||| |||||||||||| | || ||| | ||
TAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAGgttcatattggt------ctgtca--accagtttaaatgg-ccttttatttgtgtcaa-attcttattgtttgt----ctgtacttgttag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM5G811223_T01 (Zea mays), 5'ss of exon 7
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag
|||||| |||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||||| || |||||| | ||| | || ||| || | | || ||| ||||| ||| || | |||| || | || ||| | ||
GAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg---------ttctgttaatcagtttaaatggccttgtatttgtgtcaa-attttcattgcttgt----ctgtacttgttag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA17G00480.1 (Glycine max), 5'ss of exon 19
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag
|| |||||| ||||| || || || || ||||||||||| || ||||| |||||||||||||| |||||| | || || || ||||| ||||| ||||| || | | | ||| ||| | || | || | || | ||||| || | | |||| | || | | |||
GAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAGCTAATGTTCCAAAAgtgagtttattttatcaactaccatagttcttctcttctgat----ttgatgtgg-----tttgtgagatcatttcactttggttgagcag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA09G00430.2 (Glycine max), 5'ss of exon 19
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaat--gttcttattgttttttccccttctcttatcag---
||||||||||||||||| |||||||| |||||||||| || ||||||||||| |||||||| || ||||| |||||| | || || ||||| || ||||| | | || |||| |||| | | || | || | | ||| || ||||| || | |
AAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTACCGAAGgtaagcttctgctt----ttaacattttctatttatataattttttcagtttttccagttaatgcttgatgcattttctggttgcttggtttacag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA12G37100.1 (Glycine max), 5'ss of exon 19
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaat--gttcttattgttttttccccttctcttatcag---
||||||||||| ||||| |||||||| |||||||||| || ||||||||||| |||||||| || ||||| |||||| | || || ||||| |||||||| | | ||||||| ||||| | | || | || | || || || ||||| || | |
AAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTGCTAATGTTCCAAAGgtaagcttctgttt----ttagcatttgccatttttataatttttccagttttcccagttaatttttgatgcattttctggttgcttggtttacag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GLYMA07G40300.1 (Glycine max), 5'ss of exon 19
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag
| |||||| ||||| ||||| || || ||||||||||| || ||||| |||||||||||||| |||||| | || || || || |||||||| ||||| || | | | ||| ||| | || | || | || || | ||| | | |||| | || || | |||
AAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTGCAAATGTTCCAAAAgtgagtttattttatcaactaccatagttcttctcttctgatt---------tgacgcggtttgtgagatgatttcactttgactgagcag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgt-------ttacattaaaaaaaagctagcat-tgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag
|| ||| | || || ||||| ||| | | ||||||||||| ||||| || ||||||||||| |||||| | || ||||| || || ||||| |||||||| | || || | | | | | ||| || | | | ||||| | || ||| | | | |||| | |||
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattact-cgatcacattactaaatctgtgacttc----aacag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtt--tacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag
|||||||| ||||| |||||||| || |||||||||| || ||||| |||||||||||||| |||||| |||| || || || || ||||||||||| || | || ||| | | || |||| | || | || | | || |||| || || | | | |||
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv03s0110g00120.t01 (Vitis vinifera), 5'ss of exon 4
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtt--tacattaaaaaaaagctagcattgctcat---ttcattggaccctgtcattgtggcaatgttctt-attgttttttccccttctcttatcag
||| | ||||| |||||| | || |||||||||| || | ||| |||||||||||| | |||||| ||||||| || || || ||||||||||| | | || ||| | | || |||| || | | ||| || | | | ||||| ||| | || || |||
----CCTACAGATCCAGAAGAACAGCTCCGATGGATGTCTCAAGCAGTGCGTGGTTATGTTCAAGCTGTTCTGAATAGCCTTGCTGCCAATGTCCCAAAATTCGgtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctcttagtattctttattacctgttgtggttgagcaggcag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 5'ss of exon 19
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttaca-ttaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag
|||||||| || || |||||||||||| |||||||||| || ||||| ||||| |||||||| || ||||| || |||||||| || |||||||| || || || || | | |||| | || || | | |||| | | |||| | || | | | | || |||
AAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTGCTAATGTCCCTAAAgtaagcacttgtccctgaattctcatt-tttgcatctttacatctggtcact-tacaaatgcttgaat---atgtgatcgattggttggcag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv03s0038g00540.t01 (Vitis vinifera), 5'ss of exon 4
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtt--tacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag
||| || | ||||| |||||||| || | |||||||| || ||||| |||||||||||||| |||||| |||| || || || || ||||||||||| ||| | || ||| | | || ||| || | ||| | | | | ||||| | || ||| || | | |||
AAGAACTACAGATCCAGAAGAAGAGCTCCGTTGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgttggtttgttttcttaaatccattatgattca------tgtattttgttgcttatgtagttctcttagtattctttattac-ctttgagcag

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
lower sequence: PP1S38_177V6.1 (Physcomitrella patens), 5'ss of exon 18
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtt--tacattaaaaaaaagctagcattgctcattt---------cattggaccctgtcattgtgg-caatgttcttattgttttttccccttctcttatcag----------------------------------
|||||| | ||||||||||| || | ||| ||| | || |||||| | | |||||||||||| |||||||| ||||||||||| ||||| || || || | |||| || | | | | || || | || | | |||||||| ||| | || | || |
AAGACCTACAGATCCTGAAGAGGATTTAAGACTCATGGCACAGGAAGTTAGAGATTATGTTGAGGCAGTTTTGAACAGTCTGGCAGCCAATGTTCCCAAAgtaagtgcatttttaatttattttttctacaaaattatgaatgactatcagtttgcagaataatagacaatgttccgattatgcttgtcgtaagcggtactaatctaagcgatttattcccacctttcgtatgtcag

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|29662868|gb|CB659143.1|CB659143
EST:     CTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAG                         GCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
genomic: CTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacatta ... ctcttatcagGCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
EST: gi|325493116|gb|JG457640.1|JG457640
EST:     GTGGTTATGTTGAGGCTGTATTGAATAGTCTGGCAGCAAATGTCCCAAAG                         GCTATTGTGTTGTGCCAAGTGGA
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacatta ... ctcttatcagGCTATTGTGTTGTGCCAAGTGGA
EST: gi|29614012|gb|CB619025.1|CB619025
EST:     GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAG                         GCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacatta ... ctcttatcagGCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
EST: gi|29657562|gb|CB653837.1|CB653837
EST:     GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAG                         GCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacatta ... ctcttatcagGCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
EST: gi|58652777|gb|CK041457.1|CK041457
EST:     GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAG                         GCTATTGTGTTGTGCC
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacatta ... ctcttatcagGCTATTGTGTTGTGCC
EST: gi|86482222|gb|CI124855.1|CI124855
EST:     GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGCCAGCAAATGTCCCAAAG                         GCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacatta ... ctcttatcagGCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
EST: gi|218497504|gb|FG955306.1|FG955306
EST:     GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAG                         GCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacatta ... ctcttatcagGCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
EST: gi|29622848|gb|CB627859.1|CB627859
EST:     GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAG                         GCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacatta ... ctcttatcagGCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
EST: gi|25798429|gb|CA754390.1|CA754390
EST:     GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAG                         GCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacatta ... ctcttatcagGCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtttacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT