Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGATTTGGAACCATGGCAACAATCTGGCTATTTGGCAATTTTGCGCAATCTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttctatgtcagacacacctgtaaaacttctttttatctgccatttttacattacgggctaattttatttctaggattaaaccaattaaaaatt...

Basic information

species Oryza sativa
transcript LOC_Os05g39110.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g39110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G173874_T01 (Zea mays), 5'ss of exon 3
TAGATTTGGAACCATGGCAACAATCTGGCTATTTGGCAATTTTGCGCAATCTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttctatgtcagacacacctgtaaaacttctttttatctgccatttttacattacgggctaattttatttctaggattaaaccaattaaaaatt---
|||||| |||||||||||||||||||||||||||||||| ||||| || || || |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||| |||  || |  ||    || || || | ||    ||| |    |   |||  || ||| ||  |  |     |  ||   || |   
TAGATTCGGAACCATGGCAACAATCTGGCTATTTGGCAACTTTGCTCAGTCCTTTCTACAAAGCTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgcttcctatgttagatgcaaccttatc-ttttttcttttgtgttgatttgatgcaaaatgct--ttatatatcaggagtgccctctgttttgaaatagg

upper sequence: LOC_Os05g39110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA03G07550.1 (Glycine max), 5'ss of exon 3
TAGATTTGGAACCATGGCAACAATCTGGCTATTTGGCAATTTTGCGCAATCTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgta--tgctttctatgtcagacacacctgtaaaacttctttttatctgccatttttacattacgggctaattttatttctaggattaaaccaattaaaaatt
||  ||| |||  || ||||  | ||||||  ||   ||||||   ||||| ||||||||||| |||||||| |||||||| || |||||||| || |||||   | |||  | |||       |  | |  |  | |||| |   |   |       |  |    ||  ||||  ||   || | ||   |||       |
TAAGTTTAGAAGTATTGCAAGCACCTGGCTTCTTACAAATTTTCTTCAATCCTTCCTACAAAGCTCTGGTGCTTTTGAAGTATATTGCAATGGCGACTTGgtgagtacttggtctgtgctggctagttatttacatactttctgggtcataggacgggaggatccccttcttttggttt--ggttcaagagaatgggcgggt

upper sequence: LOC_Os05g39110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G47300.1 (Arabidopsis thaliana), 5'ss of exon 3
TAGATTTGGAACCATGGCAACAATCTGGCTATTTGGCAATTTTGCGCAATCTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgct-ttctatgtcagacacacctgtaaaacttctttttat-ctgccatttttacattacgggctaattttatttctaggattaaaccaattaaaaatt
|||||| ||  |||||||  | |  |||||  |||| || ||   ||| |||||  | |||||||||||||| |||||||||  |||||||||||| |||||  | | || | | ||  |  ||    |  |   || | | |  ||  |   |||   | |    | |||   || | | |  ||   |||          
TAGATTCGGGTCCATGGCTTCCACTTGGCTTCTTGGTAACTTCTTGCAGTCTTTTTTGCAAAGTTCTGGTGCTTTTGAAGTTAGCTGCAATGGAGAATTGgtcagttcttttttctcttatgcatggttgcagtatcatatcacactctcggctttggctaat---caaatccaatgttttgtgttg--ccag---------

upper sequence: LOC_Os05g39110.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv08s0105g00440.t01 (Vitis vinifera), 5'ss of exon 3
TAGATTTGGAACCATGGCAACAATCTGGCTATTTGGCAATTTTGCGCAATCTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttctatgtcagacacacctgtaaaacttctttttatctgccatttttacattacgggctaattttatttctaggattaaaccaattaaaaatt-
||| |||||||||||  |||| |  |||||  |||| || ||    ||||| |||||||||||||||||||| |||||||| ||||||||||| || ||||||   | |     |     |    | |     |||||||| |      | | || |||| | | | | |   |    ||| |   ||  | |||  |   
TAGGTTTGGAACCATTTCAACCACTTGGCTTCTTGGAAACTTCCTTCAATCCTTCCTACAAAGTTCTGGTGCTTTTGAAGTGTACTGCAATGGTGAATTGgtaaagtcttatctttgcttagctatttcttttttctttttgttctttttatataaattaagaggttactac-tcagcagggtgctacttagtaaggaaaa

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|88280508|gb|CI401706.1|CI401706
EST:     ACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: ACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|163921094|gb|EG714093.1|EG714093
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|86878408|gb|CI319631.1|CI319631
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTAC-GCAATGGAGATTT-                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|89190354|gb|CI015319.1|CI015319
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|163926652|gb|EG713668.1|EG713668
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|163920369|gb|EG711744.1|EG711744
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|88378356|gb|CI553908.1|CI553908
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|88205706|gb|CI205555.1|CI205555
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|3762102|gb|C99350.1|C99350
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|29667897|gb|CB664172.1|CB664172
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|88847448|gb|CI015941.1|CI015941
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|86250954|gb|CI013964.1|CI013964
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|88506768|gb|CI434274.1|CI434274
EST:     CTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|33799656|gb|CF325691.1|CF325691
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|27545690|gb|CA767121.2|CA767121
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|88442386|gb|CI541593.1|CI541593
EST:     ATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: ATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|88284643|gb|CI406089.1|CI406089
EST:     TGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: TGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
EST: gi|58596493|gb|CK007021.1|CK007021
EST:     CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTG                         GTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG
genomic: CTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttc ... cacttttcagGTTTTCTCAAAATTAGCTGAGCAGAGGTTCCCTAGTGAGTTTGAACTGCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGATTTGGAACCATGGCAACAATCTGGCTATTTGGCAATTTTGCGCAATCTTTCCTACAAAGTTCTGGTGCCTTTGAAGTTTACTGCAATGGAGATTTGgtatgctttctatgtcagacacacctgtaaaacttctttttatctgccatttttacattacgggctaattttatttctaggattaaaccaattaaaaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT