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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcttggtttctttatataacgtgttgtattttctctcatagttatctttgaccattctttatctcttgattcttattttcaacatacttgaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGAACTTGAAAGACAGTGTCGAAAAAGATACTTTCTTCCGCAAACTTCCAAA

Basic information

species Arabidopsis thaliana
transcript AT2G40730.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 8
-gtcttggtt-tctttatataacgtgttgtattttctctcatagttatctttgaccattctttatctcttgattcttattttcaacatacttgaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGAACTTGAAAGACAGTGTCGAAAAAGATACTTTCTTCCGCAAACTTCCAAA
  | ||| |  |  | || |    |  |     | ||   |||  | |||   | | || |  ||   || ||| | | |||     || |   ||  ||||||||||| ||||||||| |||| ||||| |||||||| ||||| ||||| |  |||||||| ||||| || ||||| || ||||||||||| ||||||||
acttttgatagttatcatttgttttagtcctgatcctgatataagtctctgcaatcctt-tccatgaatttattttgagtttgtcagtaat-acatgtgcagAGTATTTTCAAAATAAGTTGGTAGACACAATACATTTCATGGAAATTCTTAGTTTGAAAGATAGTGTTGAGAAAGACACCTTCTTCCGCAAGCTTCCAAA

upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G47590.1 (Glycine max), 3'ss of exon 8
---gtcttggtttctttatata-acgtgttgtattttctctcatagttatctttgaccattctttatctcttgattcttattttcaacatacttgaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGAACTTGAAAGACAGTGTCGAAAAAGATACTTTCTTCCGCAAACTTCCAAA
    ||||| |||  | || |  |    ||||  |||   | ||| || |||   | |||    | | | | | ||    ||||| | |    || ||  ||||| ||||| ||||||||| |||| ||||| |||||||| ||||| ||||| |  |||||||| ||||| || | ||| || ||||||||||| ||||||||
cttttcttgttttgatgattttcatagtttgtgcttttgat-ataattttctgcaatcatatcctttttatagtttgagtttttcgataa---tggatatgcagAATATTTTCAAAATAAGTTGGTAGACACGATACATTTCATGGAAATTCTCAGTTTGAAAGATAGTGTAGAGAGAGACACCTTCTTCCGCAAGCTTCCAAA

upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G38740.1 (Glycine max), 3'ss of exon 8
gtcttggtttctttatataacgtgttgtattttctctcatagttatctttgaccattctttatctcttgat--tcttattttcaacatacttgaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGAACTTGAAAGACAGTGTCGAAAAAGATACTTTCTTCCGCAAACTTCCAAA
 | ||| |   | |     ||   | || ||| |  |     | || ||   | ||  | |   | || ||  | | | |||    ||| | | ||  ||||| ||||| ||||||||| |||| ||||| |||||||| ||||| ||||| |  |||||||| ||||| || | ||| || ||||||||||| ||||||||
-ttttgatgattgtcatagactcatagtttttgcctttgatataattttctgcaatcatatccgttttaatagtttgagtttttcaataat-ggatatgcagAATATTTTCAAAATAAGTTGGTAGACACGATACATTTCATGGAAATTCTCAGTTTGAAAGATAGTGTGGAGAGAGACACCTTCTTCCGCAAGCTTCCAAA

upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 8
--gtcttggtttctttatataacgtgttgtattttctctcatagttatctttgaccattctttatctcttgattcttattttcaacatacttgaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGAACTTGAAAGACAGTGTCGAAAAAGATACTTTCTTCCGCAAACTTCCAAA
   |||| |  ||  | | |  | | ||    || |  || |  ||   |||  || || ||| | |  ||  |  || |||||  | |  || ||||||||| ||||||||||||||| | ||||| || |||||||| ||||| ||||| || ||||| |||||||| ||||| ||||| |||||||| || ||||||||
atttctttgcctcagtctctttcttcttagtattcccttctttcttcctttt--cctttttttttttggtgcctactaatttcagaagatatgcattggcagAATATTTCCAAAATAAGTTAGTGGATACTATACATTTCATGGACATTCTTAATTTGAAGGACAGTGTTGAAAAGGATACCTTCTTCCGTAAGCTTCCAAA

upper sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S47_172V6.1 (Physcomitrella patens), 3'ss of exon 8
gtcttggtttctttatataacgtgttgtattttctctcatagttatctttgaccattctttatctctt-gattcttattttcaacatacttgaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGAACTTGAAAGACAGTGTCGAAAAAGATACTTTCTTCCGCAAACTTCCAAA
 |  | | ||    | ||       |   |||||| |  ||| | |  ||| | ||      |  |   ||   | | |    ||     |  | | ||||||| |||||| |||||||||||||| || ||||| |||||||| ||||||||||| || |||||||| || ||||||   ||||| ||||| ||||| | 
atactaggttgggcagatggtagaatac-ttttcttttctaggttttgttgccgatgaaaactagcaaagaaagtgactgatgactgttattgactagcagAGTTTTTCCACAATAAGCTGGTGGAAACTATACAATTTATGGAAATTCTGAACTTAAAGGACAGTGTAGAGAAAGATGTCTTCTTTCGCAAGCTTCCTAC

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|86065920|gb|DR361677.1|DR361677
EST:     TTCCATGCCTTCTCGCAGATTGAACACCTCAAAACTTCTAGAAAATGGCG                         AGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGA
genomic: TTCCATGCCTTCTCGCAGATTGAACACCTCAAAACTTCTAGAAAATGGCGgtaatcttcc ... gaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgaccattctttatctcttgattcttattttcaacatacttgaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGAACTTGAAAGACAGTGTCGAAAAAGATACTTTCTTCCGCAAACTTCCAAA
                   tcttgat  putative branch site (score: 4)
                     ttgattcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttggtttctttatataacgtgttgtattttctctcatagttatctttgaccattctttatctcttgattcttattttcaacatacttgaattggcagAGTATTTCCAAAATAAGCTGGTGGACACCATACATTTTATGGATATTCTGAACTTGAAAGACAGTGTCGAAAAAGATACTTTCTTCCGCAAACTTCCAAA

- - - - - - - - - - - - - - - - tctctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacata