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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctacatgtgacaacagatggaaacaataggtctccttagtatgatatggctgttcaattgagctagtcaggctgatgtgttttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG

Basic information

species Arabidopsis thaliana
transcript AT3G06670.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06670.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA17G03570.1 (Glycine max), 3'ss of exon 13
------tctacatgtgacaac-agatggaaacaataggtctccttagtatgatatggctgttcaattgagctagtcaggctgatgtgttttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
        |   |||       | ||| |||   | |   |  ||| | |   || | |  | | |  |  ||||      | |    | | ||      | |  |||| |||||||| ||||| ||||||||||| ||||||||||| ||| |||| |||||||| || ||||||||
tggctgcatttctgtagtgcttaaatgtaaatgct-gccttgtttaatctaccatagattcttattctaaatagt------gtttgcctcttatgtgagatgagcagGTTTATTTCTTACACGAGTTTTGTAGTTTGAGCAAGAGCCTGCAGATGGTCCAGCAGCTTCGGCTTTTTAG

upper sequence: AT3G06670.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA07G37040.1 (Glycine max), 3'ss of exon 11
tctacatgtgacaacagatggaaacaataggtctccttagtatgatatggct-gttcaattgag--ctagtcaggctgatgtgt---tttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
|||   | ||     |  |     | ||||  ||     |||     || || ||| ||| ||    || ||    |  ||| |   ||| ||      | || |||| |||||||| ||||| ||||||||||| ||||||||| | ||| |||| |||||||| || ||||||||
tct-tgtatggttgtattt-----ctatagtgcttaaatgtaaatgctgccttgtttaatcgattcttattctaaatactgtttgccttttatgtgggatgaacagGTTTATTTCTTACACGAGTTTTGTAGTTTGAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTTTTTAG

upper sequence: AT3G06670.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA15G15270.1 (Glycine max), 3'ss of exon 12
tctacatgtgacaacagatggaaacaataggtctccttagtatgatatggctgttcaattgagctagtcaggctgatgtgttttcattctcttt-----aaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
     |     |   | |||  ||  | |  | |  |  ||     || | |||| | | | | |  | | | | |    ||||   ||||| |       | ||||  ||||||||||||| ||||||||||||||||||||| | ||| |||| || ||||| ||  ||||| |
---ttaaactgcttta-atgttaatgacatcttttttatgttcatgattgatgtt-actggtgattcttatgttaaatatttttgcctctctatttggtggacagGTTCATTTCTTGCACGAGTTTTGTAGTTTAAGCAAGAGCTTACAGATGGTACATCAGCTTCGGTTTTTTCG

upper sequence: AT3G06670.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G04260.1 (Glycine max), 3'ss of exon 13
-tctacat--gtgacaacagatggaaacaataggtctccttagtatgatatggctgttcaattgagctagtcaggctgatgtgttttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
  || | |   ||  ||             |   | | | |  | |||| | |||| | | |       || |      | ||| |   |  |   |  | ||||   ||||||||| || ||||||||||||||||||||| | ||| |||| || ||||| || |||||| |
aactgctttaatgttaatgccatctttttttttatgttcatgat-tgatgttgctggtaattcttat--gttaaatatttttgtctctctatttggtggacagGTCCGTTTCTTGCATGAGTTTTGTAGTTTAAGCAAGAGCTTACAGATGGTTCAACAGCTTCGGCTTTTTTG

upper sequence: AT3G06670.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv05s0077g01200.t01 (Vitis vinifera), 3'ss of exon 13
tctacatgtgacaacagatggaaacaataggtctccttagtatgatatggctgt-tcaatt--gagctagtcaggctgatgtgttttcattctctttaaat--agGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
     ||| |   |    |  |     || ||    |  | ||| | |  |||  | || |  |||   |  |  || ||     ||  || |   |||||  |||||| ||||||  | || ||||||||||||||||||||| | ||| |||| |||||||| || || |||||
-----atgagtttatcttttcagtacttaagtgatgtgtggatgttttttctgggttaactcagagtgtgctattcttattgacctttgttttaaataaatgtagGTATTTTTCTTATATGAGTTTTGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG

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|164230009|gb|ES178537.1|ES178537
EST:     CCAAGAAAAATTTG                         GTATATTTCTTGCACGAA-TTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTG
genomic: CCAAGAAAAATTTGgtatttcccg ... ctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTG
EST: gi|125299385|gb|EL313470.1|EL313470
EST:     TGCAAGGTTGAGGTCGCCTTCTACTTCTATGGAATCCAAGAAAAAATTTG                         GTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGT
genomic: TGCAAGGTTGAGGTCGCCTTCTACTTCTATGGAATCCAAGAAAAA-TTTGgtatttcccg ... ctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggctgttcaattgagctagtcaggctgatgtgttttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG
                         ggctgat  putative branch site (score: 4)
                                 tgttttcattctcttt  CT-rich tract
                                        attctctttaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctacatgtgacaacagatggaaacaataggtctccttagtatgatatggctgttcaattgagctagtcaggctgatgtgttttcattctctttaaatagGTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC