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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgtctttcttaccttgtttgacaatctagttatgttgggttgtttgttgctgaggaatccgagatatgttttacattgttcttaagattgtttctcttgatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT

Basic information

species Arabidopsis thaliana
transcript AT4G26850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G46230.1 (Glycine max), 3'ss of exon 3
gtaattgtctttcttaccttgtttgacaatctagttatgttgggttgtttgttgctgaggaatccgagatatgttttacattgttcttaagattgtttctcttgatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT
      |||| | ||   ||  ||     |||   ||||      | | ||      | || | |    | || | |    |||  | ||   || || |      ||| ||||| || || ||  | |||||||||||||| ||||||||||||||||||||| | ||||||||||||||||||||||| || ||||||||  | ||  | |
------gtctgttttgtttttgtttttg-tcttcctatgcatacatatatggatggcatgatttctgattttgatgtgttctgtggtgaatggtgatttt------gttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCACCTCAAGAAGAGGCCAACTGAGTTCCGAGTTGATAAGGTCCTTCAACCCT

upper sequence: AT4G26850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G43200.1 (Glycine max), 3'ss of exon 4
--gtaattgtctttcttaccttgtttgacaatctagttatgttgggttgtttgttgctgaggaatccgagatatgttttacattgttcttaagattgtttctcttgatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT
   | |||    | |  |  | ||||||    ||   || |||| | | || |||     ||  |       |||    | ||||||  | |  |  ||| | |||  | | ||||| || || ||||||||||||||| |||||||||| || |||||||| ||| | |||||||| ||||||||||||||||| ||||||||  | ||  | |
gtctgatttgtgtacccatttggtttgattcactttcta-gttgtgattttggttttcttgggttt----gcatgg---atattgtt--tgatgtgttttgttttg--ggtttagGTGATTCCTGGGAAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGCCACCTCAAGAAGAGACCAACTGAGTTCCGTGTTGATAAGGTCCTCCAACCCT

upper sequence: AT4G26850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G10430.1 (Glycine max), 3'ss of exon 3
gtaattgtctttcttaccttgtttgacaatctagttatgttgggttgtttgttgctgaggaatccgagatatgttttacat---tgttcttaagattgtttctcttgatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT
              |   || | |  | || |||||   ||   ||  | ||||        |      | |||||  |||   |||| ||     |||||   ||   ||| ||||| || || ||| ||||||||||| |||||||||| || |||||||||||| | |||||||| ||||||||||| ||||| ||||||||  | ||| |  
----------ggtctgatttatgtatccatttagtttgattcactttctagttgtgtttttgttttgcttgtgttt-gcatggatgttgtttgatgtgttttgttttgggtt-taGGTGATTCCTGGGGAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTTCGTGTTGATAAGGTCCTCCAGCCC-

upper sequence: AT4G26850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G02500.1 (Glycine max), 3'ss of exon 3
gtaattgtctttcttaccttgtttgacaatctagttatgttgggttgtttgttgctgaggaatccgagatatgttttacattgttcttaagattgtttctcttgatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT
      |||| | ||   ||||||     |||   ||||    | | | ||      | || | |    | || | |   ||||      | |  |||       |||| ||||| || || ||  | |||||||||||||| |||||||| |||||||||||| | |||||||| |||||||||||||| || || |||||  | ||  | |
------gtctgttttcttttgttt--ttgtcttcctatgcatagatatatggatggtatgatttctgagtttgatgtgttttgt------ggtgattt-------tgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTCCGAGTTGACAAGGTCCTTCAACCCT

upper sequence: AT4G26850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0090g01000.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtaattgtctttcttaccttgtttgacaatctagttatg--ttgggtt----gtttgttgctgaggaatccgagatatgttttacattgttcttaagattgtttctcttgatgttat-agGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT
            |  |  || |  |||  || |||   | |    | |    |||||||    |||| |   || ||   || |     ||| |   ||  ||| ||  |||||| |       | |  |||| || |||||  ||||||| ||| |||| ||||| || ||||| || ||| ||||||||||||| |||||||||||||| ||||| ||  | ||| | |
gtcagatattgattctgttcatctttagtttctttcctagttcgttgacaaattgggttttgggtttttcattgtggctgccaactggggttgtgggtttctctcaat-ttgtttgttaattcctgaccagGTGATTCCGGGTGAGTATGGGTTCATTGCCCAGCTGAATGAGGGCCGCCACCTGAAGAAGAGGCCCACTGAGTTCCGTGTGGATAAAGTCCTCCAGCCCT

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|124910980|gb|EH985060.1|EH985060
EST:     GGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGCGAAACCAAA                         GTTATCCCGGGGAAGTATGGTTT
genomic: GGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGCGAAACCAAAgtaattgtct ... gatgttatagGTTATCCCGGGGAAGTATGGTTT
EST: gi|124794772|gb|EH884451.1|EH884451
EST:     ATGTCACTGCCTGCGAAACCAAA                         GTTATCCC-GGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCA
genomic: ATGTCACTGCCTGCGAAACCAAAgtaattgtct ... gatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCA
EST: gi|124789411|gb|EH879090.1|EH879090
EST:     TGATGTCACTGCCTGCGAAACCAAA                         GTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCAC
genomic: TGATGTCACTGCCTGCGAAACCAAAgtaattgtct ... gatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCAC
EST: gi|124919162|gb|EH992942.1|EH992942
EST:     CTGCCTGCGAAACCAAA                         GTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCAC
genomic: CTGCCTGCGAAACCAAAgtaattgtct ... gatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCAC
EST: gi|124793740|gb|EH883419.1|EH883419
EST:     GGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGCGAAACCAAA                         GTTATCCCGGGGAAGTATGGTTTTCGTT
genomic: GGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGCGAAACCAAAgtaattgtct ... gatgttatagGTTATCCCGGGGAAGTATGGTTT-CGTT
EST: gi|164028358|gb|ES201637.1|ES201637
EST:     CTGCCTGCGAAACCAAA                         GTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCAC
genomic: CTGCCTGCGAAACCAAAgtaattgtct ... gatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatccgagatatgttttacattgttcttaagattgtttctcttgatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT
                                         tcttgat  putative branch site (score: 4)
                                     tttctcttg  CT-rich tract
          atatgttttacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgtctttcttaccttgtttgacaatctagttatgttgggttgtttgttgctgaggaatccgagatatgttttacattgttcttaagattgtttctcttgatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG