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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT

Basic information

species Arabidopsis thaliana
transcript AT5G18620.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 10
gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
        | |    |       ||||||||||    || |  | |    |  | |    | | |     |  | |||  | | |   ||  || ||  |||   || |||||||| ||||||||||||||  | || ||||| || |||||  | || || ||||| ||||| || ||||||||||||||||| || || || ||||| |
--------tgatctgagttctctattgttcctaagcatgttaacgtcacacataatttggtttcttcaaatcttgtgt-ttgactttgacatttatgtccattc-ta-cagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 10
gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
        | |    |       || |||||||    || |  | |    |  | |    | | |     |    |||  | | |   ||  || ||  |||   || |||||||| ||||||||||||||  | || ||||| || |||||  | || || ||||| ||||| || ||||||||||||||||| || || || ||||| |
--------tgatctgagttctctatggttcctaagcatgttaacgtcacacataatttggtttcttcaaatctcgtgt-ttgactttgacatttatgtccattc-ta-cagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------------gtattcattaacgcaaacaaataattgttcctatctttgatt-------ccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
                                                 || |   |||    | |  |   |    ||       |||         |  |    || | | | | |||  |||        |  |||||     ||  | || |     |  |||||||| ||||||||||||||  | || ||||| || |||||| | || || ||||| || || |||||||||||||| ||||| || || || ||||| |
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgacatagcaccatcctg-cagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 10
--------------------------------------------------gtattcattaacgcaaacaaataattgttcct---------atctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgc-tcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
                                                  || |  |||     | |  |   |  | || |         | | |     |  |    || | | |   ||  ||||     |  |  |  ||     ||  | || |||||     |||||||| ||||||||||||||  | || ||||| || |||||| | ||||| ||||| || || ||||| |||||||| ||||| || || || ||||| |
gtgattgttttccattgccatgcagatttgaatgcattattcgttagcaagtgtgtattgggagatatcagacaccgctcgtgggatgctgagcatgtgcacagtgcacctcattaagcactcgcttgtcctataattttcctttgtctgacatcgcatcatcctg--cagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGAGGTTATCAGTATTGTCGAATTGACGGAAATACAGGTGGAGAAGATCGTGATGCAT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 10
gtattcattaacgcaaacaaataattgttcctatctttgattccttt---tttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
    ||| |   |   |  |||||   ||| |  |  | ||  || |   | | | | |   |||   || |  | ||||| |   |  |    | | ||    |||    |||||||| |||||  | || || || || ||||| || |||| |||||| ||||| || || || |||||||||||||||||||| ||||| ||||||||||
---gtcagttctgtgtaggaataag-attcttggcactaatagctatgactgtgttatttcaatcagcctagtgtatttgttccattctcgcttaatctgtggttcttctccagATGACTAGGCTGCTAGACATACTTGAAGATTATCTCATGTTTCGTGGATACCAATATTGTCGCATTGATGGAAATACTGGTGGAGACGATCGAGATGCTT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 10
-----------------------------gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
                               | | || |  |  || |  | ||  ||   | | |   ||  |||  ||| | | || |||  |||     |||     | | || |   | | | |  |||    |||||||| |||||  | || || ||||| |||||  || ||| |||||| || || || ||||| |||||||||||||||||||| || || ||||||||||
gtcagttctgtcagagtgtgtgattcttgtcactgatgattgtgaataccttatattttgcaacctgtttttgtttgctctcatttatttctgccttttgaattttcttctgtgcctaatttgtggtttttctcc-ccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT

upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 10
---------------------------gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
                               | || |  |  ||    | ||  ||   | | |   ||  |||  ||| | | || |||  |||     |||     | | || |   | | |||  |||    |||||||| |||||  | || || ||||| |||||  |||||| |||||| || || || || || |||||||||||||||||||| || || ||||||||||
gtcagttctgtcagaatgtgattcttgtcgctgatgattgtgaatgccttatattttgcaacctgtttttgtttgctctcatttatttctgccttttgaattttcttctgtacctaatttgtggcttttctcc-ccagATGACTAGGCTGCTAGACATACTCGAAGATTATTTAATGTTTCGTGGATATCAATATTGTCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT

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|125065242|gb|EL132547.1|EL132547
EST:     TTGAAGGATCGAGATTCAAGGGTTCTGATATTTTCTCAG                         ATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTAC
genomic: TTGAAGGATCGAGATTCAAGGGTTCTGATATTTTCTCAGgtattcatta ... tctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
                                         ctcatct  CT-rich tract
                        ttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG