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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcattcatcctcgcctttatatttcggtttttaatcccagtcatcttcttaagttcttggagcgactagattgatttgaatatcagatgattttgaaacctaaccacacaagttcatggtctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATACCACACTGGTCAAAGCCTGGAGAAGATAAACCAGGACACAGACCGTGATT

Basic information

species Arabidopsis thaliana
transcript AT1G02560.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g19510.1 (Oryza sativa), 3'ss of exon 8
gtcattcatcctcgcctttatatttcggtttttaatcccagtcatcttcttaagttcttggagcgactagattgatttgaatatcagatgattttgaaacctaaccacacaagttcatggtctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATACCACACTGGTCAAAGCCTGGAGAAGATAAACCAGGACACAGACCGTGATT
           |    |  | |   ||  |   ||  ||  |    ||||   |||  | |    || |||  |||||   | |||  |||||||            ||  | ||| |           |||| ||||| ||||||||||||||||| ||||| || || ||||| |||||||||||||| ||   ||| || ||||| |||   || || ||||||||||
--------catttatttccacaag-cgaatagcaactccgctggctttctattgttacttgtatcaccagaa-gatttttctgtcac-tgattttc-----------cattatttctt---------ttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATACCACACTGGGCAGCCCCTAGATAAGATCAACGTAGATACTGACCGTGATT

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 8
gtcattcatcctcgcctttatatttcggtttttaatcccagtcatcttcttaagttcttggagcgactagattgatttgaatatcagatgattttgaaacctaaccacacaagttcatggtctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATACCACACTGGTCAAAGCCTGGAGAAGATAAACCAGGACACAGACCGTGATT
                 || |     |    | |  |||     |||| |      |  | |   | || | |  |||  | | |||  | |  |||  |  ||   |      | ||  | | |   ||||| ||||| |||||||| |||||||| ||| |||| || ||||| |||||||||||||| ||   |||||| ||||| |||   || || |||||||| |
-----------------ttgttacaagccaatgagcccc-----tcttttggcaaccgagtaagaattacagttgttt--acaccagcagttgctgatcctcaagttc------tgattattttat-tcagGCCAATGAGATGCTGCACCACAAGGCGAACTTAAATGGATACCTTGCATACCACACTGGGCAGCCCCTGGATAAGATCAACGTAGATACTGACCGTGACT

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G01550.2 (Glycine max), 3'ss of exon 8
gtcattcatcctcgcctttatatttcggtttttaatcccagtcatcttcttaagttcttggagcgactagattgatttgaatatcagatgattttgaaacctaaccacacaagttcatggtctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATACCACACTGGTCAAAGCCTGGAGAAGATAAACCAGGACACAGACCGTGATT
                        |    || | ||  || |  | |    ||||      |     ||  |   ||  ||||     |  |   |||| || |  |      ||||   |       ||||| ||||||||||||||||| |||||||| || || || || ||||| || |||||||| |||||  | || ||||| |||||||| ||||||||||| |
------------------------tttacttgttatatcactgttttgtacaagtatcattaattcataattctgttataatagttcttcttcgagaaaactgattatg---attcacaattc----tcagGCTAATGAAATGCTGCATCATAAGGCAAATCTGAATGGATATCTCGCCTATCACACTGGCCAAAGTTTAGACAAGATCAACCAGGATACAGACCGTGACT

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G37880.1 (Glycine max), 3'ss of exon 8
gtcattcatcctcgcctttatatttcggtttttaatcccagtcatcttcttaagttcttggagcgactagattgatttgaatatcagatgattttgaaacctaaccacacaagttcatggtc-tgaaac-cagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATACCACACTGGTCAAAGCCTGGAGAAGATAAACCAGGACACAGACCGTGATT----------------------------
                                                     |   |||       |  |||| ||| ||  |||  | ||| | |  |   |    || | ||    ||| |||  | |||||||||||||||||||||||||||||||||||    || || ||  | || ||||||||||||||  | || ||||| |||||||| |||||| ||||||                            
-----------------------------------------------------ggatttgc--tagttttattgcttttaaagtcaagtaattctta--ctagatataactaattatcagtcatgattctcaggcaaatgaaatgctgcatcacaagGCAAACCT----GGGTATCTTTCCTATCACACTGGTCAAAGTTTAGAAAAGATCAACCAGGATACAGACTGTGATTTTTTCATGAAAGCGAAAGAAGCCAAAGA

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G01510.2 (Glycine max), 3'ss of exon 8
gtcattcatcctcgcctttatatttcggtttttaatcccagtcatcttcttaagttcttggagcgactagattgatttgaatatcagatgattttgaaacctaaccacacaagttcatggtctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATACCACACTGGTCAAAGCCTGGAGAAGATAAACCAGGACACAGACCGTGATT
                   |    | ||||| |     || |  | |    ||||      |     ||  |   ||  ||||     || |   |||| || |   |||   ||||   |       ||||| |||||||||||||||||||||||||| || || || || ||||| || || || || |||||  | || ||||| |||||||| ||||||||||| |
-------------------aaggattggtttat-----cacttttttgtacaagtatcataaattcataattctgttataatagtccttgttcaagaaaactgattgcac---ttcaaaattc----tcagGCTAATGAAATGCTGCATCACAAGGCAAATCTGAATGGATATCTCGCCTATCATACCGGCCAAAGTTTAGATAAGATCAACCAGGATACAGACCGTGACT

upper sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 3'ss of exon 8
gtcattcatcctcgcctttatatttcggtttttaatcccagtcatcttcttaagttcttggagcgactagattgatttgaatatcagatgattttgaaacctaaccacacaagttcatg--gtctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATACCACACTGGTCAAAGCCTGGAGAAGATAAACCAGGACACAGACCGTGATT
                         || | |||   | |  |    || | |    ||    |   ||  | | ||   || |  | |  |     | |||| |  |       ||||    ||      ||||||||||||||||||||||||||||| || || || || || ||| | |||||||| ||||| ||||| |||||||| ||||| ||||| || |||||||
------------------------gcgctgttttggcactttttgtttataatacact----gttgctttactcatcaaaaaaaaaaaaaa-----agacctgattagtggccatcattttatcccttctcagGCAAATGAAATGCTGCATCACAAGGCTAATCTGAATGGGTATCTCTCCTACCACACCGGTCAGAGCCTTGAGAAGATCAACCAAGACACTGATCGTGATT

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|124929583|gb|EL007115.1|EL007115
EST:     CCAAACCGACATTGACATTCAG                         GCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATAC
genomic: CCAAACCGACATTGACATTCAGgtcattcatc ... ctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATAC
EST: gi|86083420|gb|DR379179.1|DR379179
EST:     ATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG                         GCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATAC
genomic: ATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAGgtcattcatc ... ctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATAC
EST: gi|124932010|gb|EL009313.1|EL009313
EST:     CCAAACCGACATTGACATTCAG                         GCAAATGAAATGCTTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATA
genomic: CCAAACCGACATTGACATTCAGgtcattcatc ... ctgaaaccagGCAAATGAAATGC-TGCATCACAAGGCAAACCTAAACGGTTACCTCGCATA
EST: gi|125245366|gb|EL259451.1|EL259451
EST:     ATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG                         GCAAATGAAATGCTGCATCACAAG
genomic: ATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAGgtcattcatc ... ctgaaaccagGCAAATGAAATGCTGCATCACAAG
EST: gi|124962334|gb|EL036764.1|EL036764
EST:     ATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG                         GCAAATGAAATG
genomic: ATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAGgtcattcatc ... ctgaaaccagGCAAATGAAATG
EST: gi|116483047|gb|EG525639.1|EG525639
EST:     GAGCTCAAGGTGGCCAAACCGACATTGACATTCAG                         GCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATAC
genomic: GAGCTCAAGGTGGCCAAACCGACATTGACATTCAGgtcattcatc ... ctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATAC
EST: gi|124845973|gb|EH930410.1|EH930410
EST:     ATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG                         GCAAATGAAATGC
genomic: ATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAGgtcattcatc ... ctgaaaccagGCAAATGAAATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatatcagatgattttgaaacctaaccacacaagttcatggtctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATACCACACTGGTCAAAGCCTGGAGAAGATAAACCAGGACACAGACCGTGATT
                      acctaac  putative branch site (score: 2)
              attttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcattcatcctcgcctttatatttcggtttttaatcccagtcatcttcttaagttcttggagcgactagattgatttgaatatcagatgattttgaaacctaaccacacaagttcatggtctgaaaccagGCAAATGAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATACCACACTGGTCAAAGCCTGGAGAAGATAAACCAGGACACAGACCGTGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA