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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttcttcccttcaactgtctacctctttcttcagatcttgtatcaaccaattctgacttgtgatacattatgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAAAACCACTGCAAGAAGGCTGCTGCTTGAAGCT

Basic information

species Oryza sativa
transcript LOC_Os11g33240.3
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 20
--------gtatatttcttccct--tcaactgtctacctctttctt--cagatcttgtatcaaccaatt--ctgacttgtgatacattatgtatga--cagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAAAACCACTGCAAGAAGGCTGCTGCTTGAAGCT
         || || ||     |  | |    |||||  ||       |||| | |   | |  |   |  || | || || |  ||||| |||||  |||||||| ||||||||||| ||||| ||||| || || || ||||||||||| ||||||||||||||||| ||| ||||||| ||    ||||| ||||| |
caattttcttacatctcacaggtagttaggaatctacaactaaacaagcagacccttagtaattctgctggctaattt-tgtttgattatttatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAATAACAAGGCTGCCTGAAGAT

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 18
gtatatttcttcccttcaactgtctacctctttcttcagatcttgtatcaaccaattctgacttgtgatacattatgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAAAACCACTGCAAGAAGGCTGCTGCTTGAAGCT
|| |   |  | |||||   | | | |    ||  | ||   || |  |  | |||| ||  | || ||  | | | |    |||||||| ||||||||||| ||||| ||||| ||||| || || ||||| || ||||||||||||||||| ||| ||||||||||    ||||| |||||||
gtctgccttctaccttc---tctttgcacagtttctaagtaattctgccggctaattttgtttggttatttaat-tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTCGAGAGGCCCAAGAGCGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCCTGAAGCT

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G063851_T01 (Zea mays), 3'ss of exon 20
gtatatttcttcccttcaactgtctacctctttcttcagatcttgtatcaaccaattctgacttgtgatacattatgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAAAACCACTGCAAGAAGGCTGCTGCTTGAAGCT
|| |   |  | |||||   | |  |  |  ||  | ||   || |     | |||| ||  |  | ||  || |||     |||||||| ||||||||||| ||||| ||||| || || || ||||||||||| ||||||||||||||||| ||| ||||||||||    |||||||||||||
gtctgccttctaccttc---tcttgatatagtttcttagtaattctgctggctaattttgtttgattatttatgatg-----cagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAAGAACAAGGCTGCTTGAAGCT

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 19
-------------------------gtatatttcttcccttcaactgtctacctctttcttcagatcttgtatcaaccaat--------tctgacttgtgata-----cattatgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAAAACCACTGCAAGAAGGCTGCTGCTTGAAGCT
                          |    |||| || |||     | |   | |||  | | ||||   ||    |  |        ||||| |  | ||       |||   | |  ||| | || |||||||||||||||||  |||| || || || || || ||||| || ||||| ||||| ||||||||||||||||| || || || | |  ||
gttctcactatgtccctcaccttcttttctcttctccctttccgtattttgtttgttttcttaaatctctcattcttccttcgggtgcatctgaatcattattattattatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT

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|163929405|gb|EG713830.1|EG713830
EST:     ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|86504183|gb|CI146816.1|CI146816
EST:     ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|88263949|gb|CI367723.1|CI367723
EST:     TCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: TCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|89175851|gb|CI042872.1|CI042872
EST:     ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|86255614|gb|CI065291.1|CI065291
EST:     ATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: ATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|88266492|gb|CI377394.1|CI377394
EST:     ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|88255207|gb|CI354031.1|CI354031
EST:     ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|86500499|gb|CI143132.1|CI143132
EST:     ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|88247059|gb|CI246908.1|CI246908
EST:     ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|89186485|gb|CI048157.1|CI048157
EST:     ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|88828444|gb|CI073314.1|CI073314
EST:     TACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: TACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|88266394|gb|CI377296.1|CI377296
EST:     CACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: CACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
EST: gi|86480028|gb|CI122661.1|CI122661
EST:     ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAG                         CTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC
genomic: ATTACACCGTCCTTTTCGGAGTTTCGAGGAGCATAGGCATAGGATCCCAGgtatatttct ... tgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttcagatcttgtatcaaccaattctgacttgtgatacattatgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAAAACCACTGCAAGAAGGCTGCTGCTTGAAGCT
                         ttctgac  putative branch site (score: 2)
                                     atacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttcttcccttcaactgtctacctctttcttcagatcttgtatcaaccaattctgacttgtgatacattatgtatgacagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAAAACCACTGCAAGAAGGCTGCTGCTTGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC