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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtcattcctgcttataagataccagaataatgctatgaagaccgtccttggttgtcagcattcttatacacaatgataatctttgtttttcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCAGCTGCTATCGTTCTGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g08700.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08700.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G107101_T03 (Zea mays), 3'ss of exon 12
gtatggtcattcctgcttataagataccagaataatgctatgaagaccgtcct-tggttgtcagcattcttata-cacaatgataatctttgtttttcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCAGCTGCTATCGTTCTGCAG
||||| | ||   | ||||||||   || || |   | ||||||| |     | | ||||| |||||||||||  |  |||||  ||| |||||| ||||| ||||||||| ||||| ||||||||  | |||||||||||||| |||||||| ||||||||||||||||| |||
gtatgtttatgtgttcttataag---cccgagtggcggtatgaagtcatcaatattgttgttagcattcttatggctaaatgaccatccttgtttctcatgtgtagGTTGTTGATGCACTTTGTGATGTCGTTTCAGCCTCACCAACCAAGGCATCAGCTGCTATCGTTCTCCAG

upper sequence: LOC_Os01g08700.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 11
gtatggtcattcctgcttataagataccagaataatgctatgaagaccgtccttggttgtcagcattcttata-cacaatgataatctttgtttttcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCAGCTGCTATCGTTCTGCAG
                       |||      |  |  ||| |      |   | ||||| ||||||||| |  |  ||||| |||| |||||| ||| | ||||||||||||||| ||||||||  | |||||||||||||| |||||||| ||||||||||||||||| |||
---------------------gtataattatgtgttcttataagccttctttattgttgttagcattcttgtggctaaatgacaatccttgtttctcacgtgtagGTTGTGGATGCACTTTGTGATGTCGTTTCAGCCTCACCAACCAAGGCCTCAGCTGCTATCGTTCTCCAG

upper sequence: LOC_Os01g08700.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G107101_T01 (Zea mays), 3'ss of exon 12
gtatggtcattcctgcttataagataccagaataatgctatgaagaccgtcct-tggttgtcagcattcttata-cacaatgataatctttgtttttcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCAGCTGCTATCGTTCTGCAG-------------------------------
||||| | ||   | ||||||||   || || |   | ||||||| |     | | ||||| |||||||||||  |  |||||  ||| |||||| ||||| ||||||||| ||||| ||||||||  | |||||||||||||| |||||||| ||||||||||||||||| |||                               
gtatgtttatgtgttcttataag---cccgagtggcggtatgaagtcatcaatattgttgttagcattcttatggctaaatgaccatccttgtttctcatgtgtagGTTGTTGATGCACTTTGTGATGTCGTTTCAGCCTCACCAACCAAGGCATCAGCTGCTATCGTTCTCCAGGTCAAGATATTGCTATATTGCACGTTTGGTC

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|33794177|gb|CF322979.1|CF322979
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|58689941|gb|CK078628.1|CK078628
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACGTTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|88689129|gb|CI732705.1|CI732705
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|33684724|gb|CF312963.1|CF312963
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|396941313|gb|HO188522.1|HO188522
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACGTTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|38481214|gb|CF965303.1|CF965303
EST:     TGCAGAAAGTA-ATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACGTTGTTTCAGCGTCGGCGACCAAGGCTTCA
genomic: TGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|88689326|gb|CI732902.1|CI732902
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|88690745|gb|CI734824.1|CI734824
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|33793269|gb|CF322515.1|CF322515
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|29668032|gb|CB664307.1|CB664307
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|88689955|gb|CI734034.1|CI734034
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|88691766|gb|CI733343.1|CI733343
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|88690455|gb|CI734534.1|CI734534
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|88691375|gb|CI733958.1|CI733958
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|86848173|gb|CI290653.1|CI290653
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|55410210|gb|CV722586.1|CV722586
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|58611835|gb|CK039547.1|CK039547
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGAC
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGAC
EST: gi|29666878|gb|CB663153.1|CB663153
EST:     CAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: CAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|38477853|gb|CF961986.1|CF961986
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACGTTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|86885526|gb|CI318677.1|CI318677
EST:     ATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCACCCTCACCGACCAAGGCTTCA
genomic: ATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|88690675|gb|CI734754.1|CI734754
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|88689073|gb|CI732649.1|CI732649
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|29657062|gb|CB653337.1|CB653337
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|8335705|gb|BE040522.1|BE040522
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACGTTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|86905138|gb|CI289285.1|CI289285
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttggttgtcagcattcttatacacaatgataatctttgtttttcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCAGCTGCTATCGTTCTGCAG
                                   tctttgtttttcat  CT-rich tract
                               ataatctttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtcattcctgcttataagataccagaataatgctatgaagaccgtccttggttgtcagcattcttatacacaatgataatctttgtttttcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCAGCTGCTATCGTTCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG