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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgaatatttttttgtggtttgaaaagatatttgttactgcttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 4
--------------------------------gttgaatatttttttgtggtttgaaaagatatttgttactgcttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgt------gcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
                                 || |||   ||| | ||  ||  |  | ||||||   ||  ||      |   | |  |  ||| |   | ||| || ||  || ||||||      |||||| || ||||||||||| || | ||| || ||||||||||||||| | || || || ||||| |||||||| ||||| || || ||||||||||||||  
gtatatctttgcgcttttatgtgcaaatgcttatttaatccctttatctgcctttcaggg-tatttg--gctattttgttgcctagtttcactagcattttcttattttaaat-tctgtcatgtatttgagcagTTCAAGCAAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGT

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 4
--------------------gttgaatatttttttgtggtttgaaaagatatttgttactgc-ttccaaagcctctatttcgtgcagtgagtaatt--atatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
                      ||  ||| ||    || ||   ||| |  ||||||||||  || |  |  ||| ||    |    | |   |    |||  ||  |    |||||||||||| ||||||||||| || || || |||||||||||||||||  | || || || ||||| |||||||| ||||||||||| ||||| |||| |||| 
gtatgtctctgggctctggccatgtttatgttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 4
---------gttgaa-tatttttttgtggtttgaaaagatatttgttactgcttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
         ||     ||  | |||    |  ||  |  || || | |   |||    | | ||| |   ||  |  || |||||   | | | |     ||  ||||||| ||||| ||||||||||| |||||||| || ||||||||| | || ||||| ||||| ||||| || ||||||||||| |||||||||||||| |
gtgagttttgtgaggctacatgtttactatacgattaattaatt-tgagcacttgtgtatcttctttcaagtctaaagactaattcagtgtacttgcatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 4
----gttgaatatttttttgtggtt-tgaaaagatatttgttactgcttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
    |||   |     |   || ||   | | |||   | | |  ||||  | | | |||  |  || ||  ||||||||   | | | |     ||  ||||||| ||||| ||||||||||| |||||||| || ||||||||| | || ||||| ||||| ||||| || ||||||||||| ||||| |||||||| |
gtgagttttgtgaggctacatgtttactatacgattaatttgaacgcttgtatatcttcttataagtccaaagagtaattcagtttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 2
gttgaa-tatttttttgtggtttga----aaagatatttgttactgcttccaaagcctctatt--tcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
||||   ||||| | ||  | ||      ||||||   |  ||     ||     |   ||    || |  |||  |       || |   |  ||||| |||||||||||||||||||||||||   ||||||| || ||||| ||  | || ||||| ||||||||||| || ||||| ||||| ||||| ||||||||  
gttggcctatttctctgcagatttgctataaagattgatcatatgaactcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 4
gttgaa-tatttttttg-tggtttg----aaaagatatttgttactgcttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
||||   ||||| | || || ||||    | |   ||||  || |  ||   | | | |||   ||    |||  |       || |   |  ||||| |||||||||||||||||||||||||   |||||||  | ||||| ||  | || ||||| ||||||||||| || ||||| ||||| ||||| ||||||||  
gttggcctatttctctgctgctttgctatatagattattcatttcaactcttaca-catcttcgtcaacgagtatggggaataatttattttacatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAAACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCAAACACAAATGCATGCCTCCTTGCTGAGC

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
gttgaatatttttttgtggtttgaaaa-gatatttgtt-actgcttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
||   |||     |       || | | | |  ||||  | |  ||    | | | |||||  ||        | || ||   | || |      ||||||||||||||||||||||||||   ||||||||||||||||||  |  | || || ||||||||||| || ||||| ||||||||||||||||||||||
gtgagatacacactcaatacatgtatatggttcttgtggatttgtttttcatcatttattttctg--------agttttaatggactttt-----cagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA

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|124821020|gb|EH905886.1|EH905886
EST:     TTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG                         TTTAAACAAGCTGAAGAAACAGACAAAGAAGCTTGATTTGGATGGGTTGGT
genomic: TTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAGgttgaatatt ... tcatgtgcagTTTAAACAAGCTGAAGAAACAG-CAAAGAAGCTTGATTTGGATGGGTTGGT
EST: gi|164097406|gb|ES104243.1|ES104243
EST:     ACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG                         TTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTG
genomic: ACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAGgttgaatatt ... tcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTG
EST: gi|116438055|gb|EG480647.1|EG480647
EST:     GTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG                         TTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTG
genomic: GTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAGgttgaatatt ... tcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA
                                       tgcctctc  CT-rich tract
                         tgagtaattatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaatatttttttgtggtttgaaaagatatttgttactgcttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG