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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatttctgtttaagatgatgttggtaaaaacaaaaggtttacacttaacttcacttgtttcttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA

Basic information

species Arabidopsis thaliana
transcript AT2G27860.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G167872_T02 (Zea mays), 3'ss of exon 2
---------gtaagcatttctgtttaa--gatgatg-----ttggtaaaaacaaaaggtttacacttaacttcacttgtttcttgt----gacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
         ||||   |||    |     | |||||      | ||   ||||     ||||   ||   |    ||| ||   ||    | ||||||||||||| || ||||| ||||| ||||| |||||  |||||||||| |||||||| || |||||||||||||| || ||  | ||||||||||| ||
gtcagtagagtaaaattttgcactgtgccgctgatggccttcttgttctaacacttcttttatgtttttgtcattttgatttgagtatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATTGGATTGGGCCAAGGATGGATTTCATTCCTGGTGTCGATGGTCCTAGTGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
--------gtaagcat-ttctgtttaagatgatgttggtaaaaacaaaaggtttacacttaact-------tcacttgtttcttg------tgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
         | ||| | || | |||   |   ||| | | |          | |    |||| |       ||| || ||| |||         ||||||| ||||| || ||||| ||||| ||||| |||||  ||||||| || ||||||||||| |||||||| ||||| || ||  ||||||||||||| ||
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 4
--------gtaagcatttctgtttaag-atgatgttggtaaaaacaaaaggtttacacttaacttcact----tgtttcttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
          |    ||| |||||| |  |  | ||  |             ||    | |   |||||    |||   |  || |||||||||||||||| |||||  | |||||||| || ||  | ||||||||||||||||||||| | ||||||||||| || |||||||||||||| || ||
gtgagttttgatttgtttttgtttaggtgttgtttttttttttctttttcaattttgttaattctcactgatgtgtgattattggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTGAGGCCTTTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGCATTGATGGTCCAAGTGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
--------gtaagcatttct-gtttaagatgatgttggtaaaaacaaaaggtttacacttaacttcacttgtttcttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
         |  | |||| | ||||  |   |||||  |       ||   |    | |     |    |||       | |||||||||||||||| |||||  | |||||||| || ||| | || |||||||||||||||||| | ||||||||||| || || ||||||||||| || ||
gtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 2
gtaagc-atttctgtttaagatgatgttggtaaaaacaaaaggtttaca---------cttaacttcact----tgtttcttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
|| |||   || |||||    | || ||       | | |  |||| ||         |||    |||||    ||    |  || |||||||||||||||| |||||  | || ||||| || ||  |||||||||| |||||||||||  | ||||||||||| ||||||||||||||||| || ||
gtgagctgcttttgtttggtttaattttttattgcatatactgtttccatgtcttgacctttgtctcactgagatgacattgttggcagCTGAGGGTGCTGAAAATGGCTTGGAATTCACAATTGTGAGACCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGTCCAAGTGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 4
------------------gtaagcatttctgtttaagatgatgttggtaaaaacaaaaggtttacacttaacttcact----tgtttcttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
                  ||     ||| | ||    |   ||||   |       | |  ||   |||    |||||    ||    |  || |||||||||||||||| |||||  | || ||||| || ||  | |||||||| |||||||||||  | ||||||||||| |||||||||||||| || || ||
gtgagctgattttgtttggtttaattttttattgcgtacactgtttccattttttcatgtcttgacctttgtctcactgagatgacattgttggcagCTGAGGGTGCTGAAAATGGCTTGGAATTCACAATTGTGAGGCCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGCCCAAGTGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 4
----gtaagcatttctgtttaagatgatgttggtaaaaacaaaaggtt----taca-----cttaacttcacttgtttcttgtg---acagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
    || | | ||||  |  |     | |||  | |  |     |  |    ||||     || |  || | || |||    ||   ||||||||||||||||||||||  || ||||||||||| ||  | || |||||||||||||| || || |||||||| || || ||||||||||||||||||||
gtgagtgaacttttccatcgatctgtacgtttcttagcatgcgtgtgtatcatacatccttctcatttttattttttttcattgtttacagCTGAGGGTGCTGAGAATGACCTAGAGTTCACCATTGTGAGGCCCTTTAACTGGATTGGGCCCAGAATGGATTTTATTCCTGGCATTGATGGTCCTAGCGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
----gtaagcatttctgtttaagatgatgttggtaaaaacaaaaggtttacacttaacttc---acttgtttcttgtga----------cagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
    || | | ||||  |  |    ||||||  | || |   |    |  ||   | |||    | || ||| || | |          ||||||| ||||| |||||||| || ||||||||||| ||  | ||||||||||||||||| ||||| ||||||||||| || ||||||||||||||||| ||
gtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ18978 (Selaginella moellendorffii), 3'ss of exon 4
gtaagca---tttctgtttaagatgatgttggtaaaaacaaaaggtttacacttaacttcacttgtttcttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
|||||||   ||||||||| | |           |||  ||    | |     |    | |  |  |  ||    |||| ||||| || ||||| || ||||| ||||| |||||||| || || ||||||||||| ||  |||||||||| || ||||| || ||||| || |||||
gtaagcaaagtttctgtttgaaa----------gaaactaagtcatgtggttgtggtgttatataatctttc---cagCCGAGGGAGCAGAGAACGGCCTTGAATTCACAATCGTACGTCCCTTCAACTGGATTGGGCCACGGATGGATTTTATTCCCGGGATCGATGGGCCAAGCGA

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ07025 (Selaginella moellendorffii), 3'ss of exon 4
gtaagcatttctgtttaagatgatgttggtaaaaacaaaaggtttacacttaacttcacttgtttcttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
|||||||         ||| |  |||| | || ||   ||| | |    ||    |   || |    | |  |||| ||||| || ||||| || ||||| ||||| |||||||| || || ||||||||||| ||  |||||||||| || ||||| || ||||| || |||||
gtaagca---------aagtttctgtttgaaagaaactaagttatgtggttgtggtgttttataatctttc-cagCCGAGGGAGCAGAGAACGGCCTTGAATTCACAATCGTACGTCCCTTCAACTGGATTGGGCCACGGATGGATTTTATTCCCGGGATCGATGGGCCAAGCGA

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|116380179|gb|EG422771.1|EG422771
EST:     GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
genomic: GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
EST: gi|116377085|gb|EG419677.1|EG419677
EST:     GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
genomic: GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
EST: gi|116422972|gb|EG465564.1|EG465564
EST:     GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
genomic: GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
EST: gi|116377081|gb|EG419673.1|EG419673
EST:     GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
genomic: GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
EST: gi|125307512|gb|EL321597.1|EL321597
EST:     GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGG
genomic: GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGG
EST: gi|116377084|gb|EG419676.1|EG419676
EST:     GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
genomic: GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
EST: gi|164188179|gb|EL975818.1|EL975818
EST:     GAGGTGGTCATATGCGTGTGCAAAGCAACTGATCGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACG
genomic: GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACG
EST: gi|164104386|gb|ES157209.1|ES157209
EST:     TCATATGCGTGTGCAAAGCAACTGATCGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAAC
genomic: TCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAAC
EST: gi|116377082|gb|EG419674.1|EG419674
EST:     GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
genomic: GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
EST: gi|125239238|gb|EL253323.1|EL253323
EST:     TGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
genomic: TGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
EST: gi|116377086|gb|EG419678.1|EG419678
EST:     GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
genomic: GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
EST: gi|116380174|gb|EG422766.1|EG422766
EST:     GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACG                         CTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT
genomic: GAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcattt ... cttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgttggtaaaaacaaaaggtttacacttaacttcacttgtttcttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA
                           acttaac  putative branch site (score: 3)
                                 cttcacttgtttctt  CT-rich tract
         taaaaacaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatttctgtttaagatgatgttggtaaaaacaaaaggtttacacttaacttcacttgtttcttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA