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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggatgcatgctctgtatagatgcttttatgtttgtctactctacattatctttaggatatgtgattgaaggcgatttgaattttgatattttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTTAAAGAACTTAAAGGCCATGAGAATATTGTTCACTTCTACAATGCGTTTG

Basic information

species Oryza sativa
transcript LOC_Os02g03410.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 1
tggatgcatgctctgtatagatgcttttatgt-ttgtctactctacattatctttagga-------tatgtgattgaaggcgatttgaattttgatattttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTTAAAGAACTTAAAGGCCATGAGAATATTGTTCACTTCTACAATGCGTTTG
|| | | |||||| | | || ||| || || | || |||| | | |||||| | | | ||| ||| | || || ||| |||||| ||||||||||||||||||||||| || |||||||||||||||||||||| ||||||||| ||| ||||||||||||||||||||||||| ||||
--------catattgccttgttgctttcacatattttctgttccacgtcatacttagaagttagaacacgtgatttatgccaattaagattattattttatataacagATGACCCGCCCTGTTGCTGTGGAGGATGTGAAAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTG

upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 1
----------------------tggatgcatgctctg--tatagatgcttttatgttt---gtctactctacattatctttaggatatgtgattgaaggcgatttgaattttgatattttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTTAAAGAACTTAAAGGCCATGAGAATATTGTTCACTTCTACAATGCGTTTG
| | | | | || | || | | |||||| | | | || | | || | | ||| | ||| ||| | |||| ||||||||||||| ||| |||| || |||||||| ||| |||| || ||||| | |||| ||||| |||||||||||| | ||||| ||||| ||||| ||||
gtatttatttccgtcaatgccatcggcgttcgttttggtccttaatcttataatgttttcaattcatcgtgttttgtttgtaattttaggaattattaattagttgtgctttaa-atttggtggcagATGGTTCTGCCTATTGCCGTTGAGGATGTTAAGCGAGAGGTCAAGATATTGAAAGCACTTACCGGCCATGAGAATGTGGTTCAGTTCTATAATGCTTTTG

upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 3
---------tggatgcatgctctgtatagatgctt--ttatgtttgtctactctacattatctttaggatatgtgattgaaggcgatttg--aattttgatattttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTTAAAGAACTTAAAGGCCATGAGAATATTGTTCACTTCTACAATGCGTTTG
| |||| | || | | | || | | | || | || | | | || || | | | | ||| | | || | |||| ||||||||||||| ||| |||| || |||||||| ||| |||| || ||||| | |||| ||||| |||||||||||| | ||||| ||||| ||||| ||||
gtatttccgttaatgccatcgtcgttttgctcctaaatcttataattcaattcatcgtgtttttgtttgtagtttttaggaattaattagttatgctttaaatttggtggcagATGGTTCTGCCTATTGCCGTTGAGGATGTTAAGCGAGAGGTCAAGATATTGAAAGCACTTACTGGCCATGAGAATGTGGTTCAGTTCTATAATGCTTTTG

upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 2
tggatgcatgctctgtatagatgcttttatgtttgtctactctacattatctttaggatatgtgattgaaggcgatt-----tgaattttgatattttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTTAAAGAACTTAAAGGCCATGAGAATATTGTTCACTTCTACAATGCGTTTG
| || |||| | | || ||| | || | | |||| ||| |||| | || || | | ||| | |||| ||||||||||||| ||| |||| || |||||||| ||| ||||||| ||||| | |||||||||| ||||||||| ||| | ||||| |||| ||||| ||||
---acacaaactctttttcagtgttttcttattatttatgttcccatttgttttct--tatgcggtttcgtgcattcctgaatcaatccttgaatttggtggcagATGGTTCTCCCCATTGCGGTTGAGGATGTTAAGCGAGAAGTCAAGATATTGAAAGAACTTACAGGCCATGAAAATGTGGTTCAGTTCTTTAATGCTTTTG

upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 2
---tggatgcatgctctgtatagatgcttttatgtttgtctactct-acattatctttaggatatgtgattgaaggcgatttgaattttgatattttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTTAAAGAACTTAAAGGCCATGAGAATATTGTTCACTTCTACAATGCGTTTG
| | || | | | | | | || | | | | | | | || | ||| | | | ||||| | | | |||| | ||||||||||||| ||| | || || |||||||| ||| ||||||| ||||| | |||||||||| ||||||||| ||| | ||||| ||| | ||||| ||||
gctcgttttcagggttt-tcttattatttatgttccgatttgttttcatatgaagtttcg--tgcattcttgaatcaattcttgaatttggtggcac-tggcagATGGTTCTCCCCATAGCGGTTGAGGATGTTAAGCGAGAAGTCAAGATATTGAAAGAACTTACAGGCCATGAAAATGTGGTTCAGTTCCATAATGCTTTTG

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|29641793|gb|CB646800.1|CB646800
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
EST: gi|88341932|gb|CI644269.1|CI644269
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
EST: gi|88342437|gb|CI645959.1|CI645959
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
EST: gi|58590583|gb|CF988891.1|CF988891
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
EST: gi|29644214|gb|CB649221.1|CB649221
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
EST: gi|218492077|gb|FG943382.1|FG943382
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
EST: gi|29657420|gb|CB653695.1|CB653695
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
EST: gi|88330524|gb|CI635146.1|CI635146
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
EST: gi|88310411|gb|CI659201.1|CI659201
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
EST: gi|88407152|gb|CI581239.1|CI581239
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
EST: gi|88334162|gb|CI641213.1|CI641213
EST:     ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAG                         ATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT
genomic: ACCGGGCCTCCGGTGACCGCGTCGCCGTCAAGCGCATCGACAAGGCCAAGgtactactaa ... tttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatctttaggatatgtgattgaaggcgatttgaattttgatattttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTTAAAGAACTTAAAGGCCATGAGAATATTGTTCACTTCTACAATGCGTTTG
                                    ttttgat  putative branch site (score: 4)
 atttgaattttgatat  TA-rich tract
















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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggatgcatgctctgtatagatgcttttatgtttgtctactctacattatctttaggatatgtgattgaaggcgatttgaattttgatattttatggcagATGGTTCGCCCTGTTGCTGTGGAGGATGTAAAGAGAGAAGTGAAGATTCTTAAAGAACTTAAAGGCCATGAGAATATTGTTCACTTCTACAATGCGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC