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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGAAACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG

Basic information

species Oryza sativa
transcript LOC_Os07g07560.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 11
gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGAAACCATGAA------GAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
|||||||| |   || |||       | ||||||| |  ||||  | | || | |   | ||  |      |  ||    | |||||||||| |||||||||||||||   |||| |      |||||||| ||||| || ||||| ||||||||||| |||||||| |||||||||||||| ||||      
gtctgtacta---actattc------cctccatatat-atttatattt-cttcgtccttatcttta---tttgttcccgtactatagGTTGGACAGAAACGTGGAAGATTGCATGCAAATCTAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAGTTT------

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 6
gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGA---------AACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
|||||||| | | |    ||  ||| |||| |||| | ||| || | | ||  ||   | |   |      |  |  |  | |||||||||| ||||||| |||||||          | |  ||||||||||| ||||| || ||||| ||||||||||| |||||||| |||||||||||||  |         
gtctgtactaacta----ttccctctcttc-atatatagtt-agattt-ctttattcttatattta---tttgtttctgtactatagGTTGGACAGAAACATGGAAGATTGGTTGCAGATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTTAG---------

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G508368_T01 (Zea mays), 3'ss of exon 4
-------gtctgtaccaccca---ccattttactcacttccatattttgttta-ggtctgctccatatctg-tccatgaacccttctct-taaattatagGTTGGGCAGAAACGTGGAAGA---------AACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
       |   |  |   | |   |  |  ||   | | ||    ||  | ||  ||  | |   ||| || |  ||      || | | |  | |||||||||| |||||||||||||||          | |  ||||||||||| ||||| || ||||| ||||||||||| |||| |||||||||||||||||| |         
cagaactgatggggctctcgaggtctgtactaactattccctctcttcatatatagttagatttctatgtgctttatctttatttgtttatgtactatagGTTGGACAGAAACGTGGAAGATTGCTTGTAGATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCTAGCAGCTCAATGGATTTCAG---------

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G480263_T01 (Zea mays), 3'ss of exon 7
gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGA---------AACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
|| ||||| | | |    ||  ||| |||| |||| | ||| || | | |||  |   | |   |      |  |  |  | |||||||||| |||||| ||||||||          | |  ||||||| ||| ||||| || ||||| ||||||||||| |||||||| |||||||||||||| |         
gtttgtactaacta----ttccctctcttc-atatatagtt-agattt-ctctgttcttatattta---tttgtttctgtactatagGTTGGACAGAAATGTGGAAGATTGGTTGCAGATCTAGAAGAAGTTGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAG---------

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G082099_T01 (Zea mays), 3'ss of exon 5
gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGA---------AACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
|||||||| | | |    ||  ||| |||| |||| | |||    |   ||     | | |  ||      |  |  |  | |||||||||| |||||||||||||||          | |  ||||||||||| ||||| || ||||| ||||||||||| |||||||| |||||||||||||| |         
gtctgtactagcta----ttccctctcttc-atatatagttatatttctctgttcttatatttat-----ttgtttctgtactatagGTTGGACAGAAACGTGGAAGATTGGTTGCAGATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAG---------

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 11
gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGA---------AACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
|||||||| | | |    ||  ||| |||| |||| | ||| || | | |||  |   | |   |      |  |  |  | |||||||||| |||||||||||||||          | |  ||||||||||| ||||| || ||||| ||||||||||| |||||||| |||||||||||||| |         
gtctgtactaacta----ttccctctcttc-atatatagtt-agattt-ctctgtgcttatattta---tttgtttctgtactatagGTTGGACAGAAACGTGGAAGATTGGTTGCAGATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAG---------

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G017204_T01 (Zea mays), 3'ss of exon 3
-----------------------gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGA---------AACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
                       |||||||| | | |    ||  ||| |||| |||| | ||| || | | |||  |   | ||  |      |  |  |  | |||||||||| |||||||||||||||          | |  ||||||||||| ||||| || ||||| ||||||||||| | |||||  |||||||||||||| |         
atcagaactgatgggctctcaaggtctgtactaacta----ttccctctcttc-atatatagtt-agattt-ctctgtgcttatcttta---tttgtttatgtactatagGTTGGACAGAAACGTGGAAGATTGCTTGCAGATCTAGAAGAAGATGAACAACCTAAAAAGAAGGTTAGATTAGGGAACCCAGTGGCTCAATGGATTTCAG---------

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 9
gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGA---------AACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
|||||||| | | |    ||  ||| |||| |||| | |||    |    |     | | |  ||      |  |  |  | |||||||||| |||||||||||||||          | |  ||||||||||| ||||| || | ||| ||||||||||| |||||||| |||||||||||||| |         
gtctgtactagcta----ttccctctcttc-atatatagttatatttctttgttcttatatttat-----ttgtttctgtactatagGTTGGACAGAAACGTGGAAGACTGGTTGCAGATCTAGAAGAAGATGAACAACCTAAAAGGAAGGTTAGATTAGGGAGCCCAGCGGCTCAATGGATTTCAG---------

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 11
---------gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatc-tgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAG---------AAACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
         || | |       |  || |||     ||   ||||||||||   |    |   |||  |    |||     |  | || |   | ||||||| || || || |||||         ||| |  ||||||||||||||||| |||||||||||  |||| || || || ||  |||| ||||| || |         
gttgctatggtgtttttattttaggatgttaaggtgttatctattttgtttgattacattgtgtataataagaatgctaaatcttttttacaaacagGTTGGCCAAAAGCGAGGAAGGATGCTTATAAATCTGGAAGAAGATGAGCAACCTAAGAAGAAAGTGCGATTGGGGAGTCCTGCTACTCAGTGGATATCAG---------

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 11
gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGA---------AACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
||    |     ||   ||||| |   || | |          |||  | | | | |   |   || |   |  |||  |    ||||||||||| || || ||||||         ||    |||||||||||||| || |||||||||||  ||||||||||||| ||  | || ||||| || |         
gttgtgatgtttcatatttttatttctttacttcagaccagatggtaggattccttttctttattgtaatgtcttctgcataactagGTTGGGCAAAAGCGGGGAAGATTGCTCATAAATTTGGAAGAAGATGAGCAGCCAAAGAAGAAAGTACGATTAGGTAGCCCTGCGACCCAGTGGATATCAG---------

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|58659496|gb|CK048176.1|CK048176
EST:     TGATTGAGGTACCTGCCTCAAGACCTATCAGAATTGATGGCGCTCTTAAG                         GTTGGGCAGAAACGTGGAAGAAACCATGAAGAAGATGAG
genomic: TGATTGAGGTACCTGCCTCAAGACCTATCAGAATTGATGGCGCTCTTAAGgtctgtacca ... taaattatagGTTGGGCAGAAACGTGGAAGAAACCATGAAGAAGATGAG
EST: gi|58656539|gb|CK045219.1|CK045219
EST:     ATTGAGGTACCTGGGGGTCAAGACCTATCAGAATTGATGGCGCTCTTAAG                         GTTGGGCAGAAACGTGGAAGAAACCATGAAGAAGATGAGCAACCCAAGAAG
genomic: ATTGAGGTACCT--GCCTCAAGACCTATCAGAATTGATGGCGCTCTTAAGgtctgtacca ... taaattatagGTTGGGCAGAAACGTGGAAGAAACCATGAAGAAGATGAGCAACCCAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGAAACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG
                                    cccttctctt  CT-rich tract
                                       ttctcttaaattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtaccacccaccattttactcacttccatattttgtttaggtctgctccatatctgtccatgaacccttctcttaaattatagGTTGGGCAGAAACGTGGAAGAAACCATGAAGAAGATGAGCAACCCAAGAAGAAAGTTAGATTAGGTAGCCCAGCAGCTCAATGGATTTCTGTTTATAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA