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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtgtagtttaagacgatattgtaagtatgatcctgaattctgagaaacagttcttcttgttagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA

Basic information

species Arabidopsis thaliana
transcript AT1G30420.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 24
gtttgtgtgtagtttaagacgatat---tgtaagtatgatcctgaattctgagaaacagttcttcttgt---------tagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA
|||||| |||      | | |||||   |    || || |  |      | | |||   || || | ||          |||  | ||  |||| ||| | ||||| |||| ||| ||||||||||| || |||||||| || || |||||||| ||| |||||||||||||    |||||
gtttgtttgtgaaaatacatgatatatcttctcgtttgcttttcttacatcataaatgttttttttggtactattgtccagGTTCTGTTCGATTTAATCTGGATCCTTTTAATGAGCACAATGATGCGGATCTCTGGGAAGCGCTTGAAAGGGCTCATCTAAAAGATGTCATAAGGAGGAA

upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 23
---------------gtttgtgtgtagtttaagacgatattgtaagtatgatcctgaattctgagaaacagttctt-----cttgttagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA
                |   ||| ||| |   |  | |  | |   |   | | ||  ||  | |||| | || ||     | | | |||  | ||  | || ||| | ||||| |||| ||| ||||||||||| ||||||||||||||||| |||||||| ||| |||||||||| ||    |||||
gtatgctagtgaaaaatacatgt-tagctgctggagcttctttttttggcaacttgggtttagtgaaatatttattaatgccctttcagGTTCTGTTCGGTTTAATCTGGATCCCTTTAATGAGCACAATGATGCGGACCTCTGGGAGGCTCTGGAAAGGGCTCATCTAAAAGATGTTATAAGGAGGAA

upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 25
---------------------------gtttgtgtgtagtttaagacgat-attgtaagtatga-tcctgaattctgagaaaca--gttcttcttgttagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA
                           | |||||  ||      |   || |   | ||||  | | ||   |||| | ||  |    ||||  | ||||| || ||  | |||||| | |||||||||| ||||||||||||||||||||| ||| | ||| |||||||||||||| | || ||||| ||    || ||
acattgtattatcttaaattttcccttggttgtgaataaacattgtttattagcttcagtaaaacttctcccttctaaaaattatcactctttctcttagGAACTGTTCGTTTCAATCTTGATCCATTTAATGAACACAATGATGCTGACCTATGGCAAGCTTTAGAAAGGGCGCATTTGAAGGATGTAATAAGAAGAAA

upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 3'ss of exon 24
-------------------------------gtttgtgt-gtagtttaagacgatattgtaagtatgatcctgaattctgagaaacagttcttcttgt-tagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA
                                  | |||  ||||  |    ||||| || |||    |  |  | |    | |    ||    ||||  ||| || || ||||| ||| | ||||| || | |||||||||||| |||||||| ||||||||| |||| ||||| ||| | || |||||||||   || ||
ttttcccttatacattggtgtccagggttacagctatgtcatagtacacttggatatggtgagtt--gtgttatactaatggcagttttttactttgtgcagGAACTGTAAGATTTAATCTTGATCCTTTCAATGAACACAATGACGCTGACCTTTGGGAGGCTTTAGAGAGGGCACATCTCAAGGATGTCATCAGGAGAAA

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|86073144|gb|DR368901.1|DR368901
EST:     TTTGCGTAGGGTCCTAAGTATCATACCCCAGTCACCAGTTCTTTTTTCAG                         GGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACC
genomic: TTTGCGTAGGGTCCTAAGTATCATACCCCAGTCACCAGTTCTTTTTTCAGgtttgtgtgt ... ttcttgttagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagacgatattgtaagtatgatcctgaattctgagaaacagttcttcttgttagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA
                                          ttcttcttgtt  CT-rich tract
       atattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgtgtagtttaagacgatattgtaagtatgatcctgaattctgagaaacagttcttcttgttagGGACGGTGAGATTCAATATCGATCCATTTAGTGAACACAATGATGCTGACCTCTGGGAGGCTCTAGAAAGGGCGCATATAAAAGATGTCATCGATAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG