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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcattcccaatttttcttctttcaatcgaatttgttggaaaatattttgctctttggtgaaaaaaattgatcatttgttggaactttgggtttgtg...

Basic information

species Arabidopsis thaliana
transcript AT2G38880.7
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 2
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcattcccaattt------ttcttctttcaatcgaatttgttggaaaatattttgctctttggtgaaaaaaattgatcatttgttggaactttgggtttgtg------------------------------------
|||||||||| ||  | ||  |||| || ||||| |  || || |||||||| || || ||||| |||||||| |||||||||  |||||||||||||||||| |     |   |         ||||  ||         ||||||| ||    ||||   |   ||  |     ||     || | |||   |||| |||                                        
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCCGAGTTCATCTCCTTCATCACTAGCGAgtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaa----tttggagtggcgttcagggctttagc--ttggctggggttttgtgttgacttgtccatgtccacgtttttttgtccgctctttgcag

upper sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G064426_T02 (Zea mays), 5'ss of exon 2
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcattcc---------caatttt---tcttctttcaatcgaatttgttggaaaat-attttgctctttggtgaaaaaaattgatcatttgttggaactttgggtttgtg-----------------------------------
|||||||||| ||  | ||  |||| || ||||| |  || || |||||||| || || ||||| |||||||| |||||||||  |||||||||||||||||| |     |           | | |   |||||| |          |||||| || | |   ||   ||| |  ||    | |     || | |||   |||| |||                                       
TCATGAAGAAGGCCATCCCGGCTAACGGGAAGATCGCCAAGGACGCTAAGGAGACCGTGCAGGAGTGCGTCTCGGAGTTCATCTCCTTCATCACTAGCGAgtaagtccctcggccgcggctgactctgactcttctgtttgcttggcatgttgggaattcagagtggcgtttcgcaaaccgcactttagcttaggtggggttttgtgttgacttgtctacgtccacgttccttgtctgctgtttgcag

upper sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G34050.1 (Glycine max), 5'ss of exon 1
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgt------------atgcattcccaatttttcttctttcaatcgaatttgttggaaa-atattttgctctttggtgaaaaaaattgatcatttgttggaacttt---gggtttgtg----------------------------------------------------------
| |||||||| ||  ||||||| || || ||||||| ||| ||||| || || ||  | ||||||||||| |||||||||||||||||||| || |||||||            || |||  |||  |    |  |||   |  | || | |  |||  | ||||  | |||  || |  |      |  ||| ||   | |||   ||| ||| |                                                          
TTATGAAGAAGGCTCTGCCTCCCAACGGCAAGATTGCAAAGGATGCCAAAGACACCATGCAGGAATGCGTTTCTGAGTTCATCAGCTTCATTACCAGCGAgtcagttagcaactatacatatccatatcaaatgttttgtttttatttagctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcgtgcag

upper sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G33550.2 (Glycine max), 5'ss of exon 2
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgc-----attcccaatttttcttctttcaatcgaatttgttggaaaatattttgctctttggtgaaaaaaattgatcatttgttggaactttgggtttgtg--------------------------------------------------------------------------------
|||||||||| ||  ||||||| ||||| |||||||  || ||||| || || ||| | || |||||||| ||||| |||||||||||||| || |||||||  |      |||  ||| | | | | |  || |      | |   ||  | ||||| | ||| |   ||||  ||  | | |   |  | ||   | ||| |                                                                                 
TCATGAAGAAGGCTCTGCCTCCCAATGGCAAGATTGCGAAGGATGCAAAAGACACAATGCAAGAATGCGTTTCTGAATTCATCAGCTTCATTACCAGCGAgtgagtcagttattagcaactatacatatc-cagttatcgatatca-aatgttttttgttttttagctcaaaatgttttttaatg--taaagctgcagttttttaatttttattttttggggattgggggttctgagaattttttaattactgaattccacgcacgtggttattatgacttgcag

upper sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv13s0019g03600.t01 (Vitis vinifera), 5'ss of exon 2
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcat-tcccaatttttcttctttcaatcgaatttgttggaaaat---attttg--ctctttggtgaaaaaaattga-tcatttgttggaactttgggtttgtg
|||||||||| ||||||||  ||||||||||||| |  || ||||| ||||| || || || || |||||||| ||||||||||| |||||||| |||||||| ||   || |  | | | ||||||   |   |||| |  ||  ||    |||||   | |||| | ||||  ||  | || |||  |   | ||          
TCATGAAGAAGGCGTTGCCGGCTAATGGTAAGATCGCCAAGGATGCGAAGGACACTGTCCAAGAGTGCGTCTCCGAGTTCATCAGTTTCATCACCAGCGAgtacgcggatctctctctcttttcttttccttctatttctccgatgattgtgttttgggttatttgattaaaaggatgaaatcttttccttctatttctc-------

upper sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EDP06643 (Chlamydomonas reinhardtii), 5'ss of exon 1
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcattcccaatttttcttctttcaatcgaatttgttggaaaatattttgctctttggtgaaaaaaattgatcatttgttggaactttgggtttgtg--------------------------------------------------------------
| |||||||| ||| | ||    || |  || || |  || ||||| ||||| || || ||||| |||||||| |||||||| |||||||||||    ||||| |  |                |      | |   |          |    | |   |     |    |||  ||   |   |||     |  |   |                                                              
TTATGAAGAAGGCGCTCCCGAACAACGCGAAAATAGCCAAGGATGCAAAGGAGACGGTCCAGGAGTGCGTCTCGGAGTTCATTAGCTTCATCACGTCGGAgtaagtgtctgggggccccgccgctgtttggggacacggcccccgccgtcgcccccgccgtcaggagcccttgccca---gcacgaagccatgcctcacgcacagcatgcatggatgtgcagcgtaaatgcattctatgctgatatggtttgcactatgtag

upper sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S25_10V6.1 (Physcomitrella patens), 5'ss of exon 1
----TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcattcccaatttttcttctttcaatcgaatttgttggaaaatattttgct---ctttggtgaaaaaaattgatcatttgttggaactttgggtttgtg
    |||||||||| ||||||||| |||||| ||||||||  |||||||| ||||| || |||||||| || || || || |||||||| |||||||||||||||||| | ||    |       |   | | ||  |  | || | | | ||   |||   ||    | |       | ||| | |  | || |  ||        
CGCATCATGAAGAAGGCGTTGCCTGCTAATGCTAAGATTGCCAAAGATGCGAAGGAGACTGTTCAGGAGTGTGTTTCAGAATTCATCAGTTTCATCACTAgcgagtatccgtttttcacaacgtctaaataattctgacatttttgcatagatcccgctgccctcatcttacctctgctaatcttgtagttgatccatgc-------

upper sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ15374 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcattcccaatttttcttctttcaatcgaatttgttggaaaatattttgctctttggtgaaaaaaattgatcatttgttggaactttgggtttgtg
| |||||||| ||| ||||  | ||||  ||||| |  || ||||| ||||| || || || ||||||||||| ||||||||||||||||||||||||||||| | ||| |    ||   | ||||     ||   ||||  |  || || | ||  || ||                                      
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCGGAGTTCATCAGCTTCATCACTAGCGAgtaagtattgc----ttcgatcctttgtggtga---tgtta-actatcttcttctactttgtag------------------------------------

upper sequence: AT2G38880.7 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ24973 (Selaginella moellendorffii), 5'ss of exon 1
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcattcccaatttttcttctttcaatcgaatttgttggaaaatattttgctctttggtgaaaaaaattgatcatttgttggaactttgggtttgtg
| |||||||| ||| ||||  | ||||  ||||| |  || ||||| ||||| || || || ||||||||||| ||||||||||||||||||||||||||||| | ||| |      |||||   || |||   | || || | | ||| ||  |||    || |                                   
TAATGAAGAAGGCGCTGCCGGCGAATGCAAAGATCGCCAAGGATGCCAAGGAGACGGTGCAAGAATGCGTCTCAGAGTTCATCAGCTTCATCACTAGCGAgtaagtattgctggaagttctt---tcgatcctttgtggtg-atactatcttcttctactttgcag----------------------------------

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|164218903|gb|ES088321.1|ES088321
EST:     CTTCATCACTAGCGA                         GGCCAGTGATAAGTGTC-AAAAGAGAAAAGGAAAACTGTGAATGGTGATGA
genomic: CTTCATCACTAGCGAgtatgcattc ... tgctaatcagGGCCAGTGATAAGTGTCAAAAAGAGAAAAGGAAAACTGTGAATGGTGATGA
EST: gi|163975928|gb|ES055486.1|ES055486
EST:     GCTTCATCACTAGCGA                         GGCCAGTGATAAGTGTCAAAAAAGAGAAAAGGAAAACTGTGAATGGTGATG
genomic: GCTTCATCACTAGCGAgtatgcattc ... tgctaatcagGGCCAGTGATAAGTGTC-AAAAAGAGAAAAGGAAAACTGTGAATGGTGATG
EST: gi|47830028|gb|CK119712.1|CK119712
EST:     GATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGA                         GGCCAGTGATAAGTGTCAAAAAGAGAAAAGGAAAACTGTGAATGGTGATGA
genomic: GATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcattc ... tgctaatcagGGCCAGTGATAAGTGTCAAAAAGAGAAAAGGAAAACTGTGAATGGTGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAAGAAAGCGTTGCCTCCTAATGGTAAGATTGGAAAAGATGCTAAGGATACAGTTCAGGAATGCGTCTCTGAGTTCATCAGCTTCATCACTAGCGAgtatgcattcccaatttttcttctttcaatcgaatttgttggaaaatattttgctctttggtgaaaaaaattgatcatttgttggaactttgggtttgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT