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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtattgaccatatttttctccaatctctatagatccacttgaatgtttttagcaatcagaattgtgaatggaattggttggatagGTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGAGCTTAATAAAGATGGAAAGTCGCAAATTCCTCCTGTTGGAGTTATTCCTC

Basic information

species Arabidopsis thaliana
transcript AT2G18730.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g15090.1 (Oryza sativa), 3'ss of exon 3
gtgagtgtat-tgaccatatttttctccaatctctatagatccacttgaatgtttttagcaat-cagaattgtgaatg----gaattggt----tggatagGTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGAGCTTAATAAAGATGGAAAGTCGCAAATTCCTCCTGTTGGAGTTATTCCTC
||   |   | |||    |    | | | |  ||   ||| ||  |   || ||   |    | ||||||| | |||      | || ||    |   ||||||||||||||||||||||| || ||||||||  | |||||| | ||||| ||| ||    |    | |   | ||||||||| ||||  ||||| || |
gttctttcgtatgatggaaaacctgtactag-tcagcagaaccgttctcatattccaaaagtttcagaattctaaatacttacagtttgtaacctacctagGTTGCAGGAGGTGATGGTACAGTAGGTTGGGTGTTGGGATGTTTAGGAGACCTTTATGTTCAGAACAGGGAACCAATTCCTCCAGTTGCTGTTATACCAC

upper sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G01360.1 (Glycine max), 3'ss of exon 3
-gtgagtgtattgac-catatttttctccaatctctatagatccacttgaatgtttttagcaa--tcagaattg-tgaatggaattggt----tggatagGTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGAGCTTAATAAAGATGGAAAGTCGCAAATTCCTCCTGTTGGAGTTATTCCTC
  || |  || |      || |    || ||| |     | |  | |   || ||   |   |  |  |||| | |||||| || || |    |||| ||||||| |||||||||||||| |||||||||||  | ||||||||   ||| |||  |  | | ||      || | ||||||| || ||  | || || |
gatgggaataatattatgtactggattcaaatattagatgttatattaccatattggcaatcacgttggaatggatgaatgaaactgatcgattggacagGTTGCTGGAGGTGATGGTACAGTTGGTTGGGTATTAGGATGTCTAACAGAACTTCGTGCACAGGGTCGAGAGCCAGTTCCTCCAGTAGGGATCATACCAC

upper sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G07480.1 (Glycine max), 3'ss of exon 2
--gtgagtgtattgaccatattttt---ctccaatctctatagatccacttgaatgtttttagcaatcagaattg-tgaatggaattggt----tggatagGTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGAGCTTAATAAAGATGGAAAGTCGCAAATTCCTCCTGTTGGAGTTATTCCTC
   ||    || | |   ||| |      |  ||    || | ||  |  | | | | |||  ||||||   | | |||||| |  ||||    || | ||||||| |||||||||||||| |||||||||||  | ||||||||   ||| |||   | | | ||   |  || | |||| || || ||  | || || |
tgatggagataataatagtatgtacaggattaaaaaattagatatt-atattactatatttgacaatcacgttggatgaatgaagctggtcgattgaacagGTTGCTGGAGGTGATGGTACAGTTGGTTGGGTATTAGGATGTCTAACAGAACTTCGCACACAGGGTCGGGAGCCAGTTCCCCCAGTGGGTATCATACCAC

upper sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G22380.1 (Glycine max), 3'ss of exon 2
gtgagtgtattgaccatatttttctccaatctctataga----tccacttgaatgtttttagcaatcagaattgtgaatgga-------attggttggatagGTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGAGCTTAATAAAGATGGAAAGTCGCAAATTCCTCCTGTTGGAGTTATTCCTC
 |   | ||||  |  | | ||  |         |||||    |       | ||| |||| | ||    || | | ||| |       |||| || ||||||| || ||||||||||||| ||||||||||||  | ||||||||   | | ||| |  || | |||      |  |||||||| || ||  | || || |
ttttatttattttctttctcttattaggtgtagaatagaaatttttgtccaagtgtatttatccat--atatggcggatgaatctatgtattgatttgatagGTAGCCGGAGGTGATGGTAGTGTTGGTTGGGTATTAGGATGTCTCACAAAACTTCACGAACAAGGACGAGAACCTATTCCTCCAGTAGGGATCATACCAC

upper sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtgtattgaccatatttttctccaatc--------tctatagat---------ccacttgaatgtttttagcaat-cagaattgtgaatggaattggttggatagGTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGAGCTTAATAAAGATGGAAAGTCGCAAATTCCTCCTGTTGGAGTTATTCCTC
||  || ||| |  |||  |  || |||||         |  || |||         | | |||   |||  |   ||| |  |  | |    |   ||| || || ||||||||||||| ||||||||||| |||||||| || ||  |||||||||||||| | ||| |          | | |||||||||||||| ||||||| |
gtatgtttatcgggcattataatccccaattattttattttcatggataatactaaactagttggtggttgctgataatgctaagctatttg-gcggttgctttgacagGTTGCAGGAGGAGATGGTACTGTCGGTTGGGTGCTAGGTAGTCTTGGAGAGCTTGACAAACAGAATCGTGAACCAGTTCCTCCTGTTGGAATTATTCCAC

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|125120903|gb|EL168382.1|EL168382
EST:     CGGAAGGAGATGAATGTGCAAAAGAATGCAGAGCAAGGTTGAGGATTATG                         GTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGA
genomic: CGGAAGGAGATGAATGTGCAAAAGAATGCAGAGCAAGGTTGAGGATTATGgtgagtgtat ... ggttggatagGTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGA
EST: gi|86078363|gb|DR374120.1|DR374120
EST:     CGGAAGGAGATGAATGTGCAAAAGAATGCAGAGCAAGGTTGAGGATTATG                         GTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGAG
genomic: CGGAAGGAGATGAATGTGCAAAAGAATGCAGAGCAAGGTTGAGGATTATGgtgagtgtat ... ggttggatagGTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatccacttgaatgtttttagcaatcagaattgtgaatggaattggttggatagGTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGAGCTTAATAAAGATGGAAAGTCGCAAATTCCTCCTGTTGGAGTTATTCCTC
           aatgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtattgaccatatttttctccaatctctatagatccacttgaatgtttttagcaatcagaattgtgaatggaattggttggatagGTTGCAGGAGGTGATGGTACTGTTGGTTGGGTTCTTGGATGTCTTGGAGAGCTTAATAAAGATGGAAAGTCGCAAATTCCTCCTGTTGGAGTTATTCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG