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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatttttttttatctacattcttcttttttattatttctatgccatctactaacttttatttttttcccgttcttatcgtttgtgttacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG

Basic information

species Arabidopsis thaliana
transcript AT4G21660.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 10
------------------------------gtaagcattttttttta-----------tctacattcttcttttttatta------tttctatgccatctactaact--tttatttttttcccgttctta-tcgtttgtgttacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG
                               | | |||||||||| |            ||  |||||||||||| | |          | || |  |   || |||    | || ||| |  ||  | | |  ||  ||| | | |||||||||||||| |||||||||||||||||||||| || |||||||||||||||||||| |||
gtatatatttttttacatattcactgtttttttatcattttttttaaattgataggttccttaattcttctttttcagtgaagagtcccccattcttttatctcactgacatgttgtttacttgtcttcaattcttcatgtga-acagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCTAACTATGAG

upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 10
---------------gtaagcatttttttttatctacattcttcttttttattatttctatgccatctactaacttttatttttttcccgttctta-tcgtttgtgt-tacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG
                ||  || | ||| || | | ||||  |  |||| |  |||  || | |     ||  ||||||| |   |  | |  ||| | || |        | |||||||||||||| |||||||||||||||||||||| || |||||||||||||| ||||| |||
gtagaaattttttacatattcactgtttattttat-catttattattttaaaaattgataggtctctggct--cttttatctcactgacatgtttacttgtcttcacgcgaacagTATGGGCGTCCACTGTATGGAGATGTTTTTGGTGTTCAACAACAAGATCAGCCCAACTATGAG

upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 10
--------------------------gtaagcattt--ttttttatctac------attcttcttttttattatttctatg----ccatctactaacttttatttttttc-ccgttcttatcgtttgtgt-tacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG
                           | | |||||  ||||| |  ||        ||||   |||| ||| ||  ||       |  | ||    ||| |  |  ||  ||  | || | || ||    || | ||||||| |||||| | |||||||||||||||||||| || ||||||||||||||||| || |||
gtacattttttatattcactcttcttttcatcatttgatttttgaattattatgggtttctgaattttcatttttattaaagggctctcccaccccttttcacctcattgaccacttttcttgtctgcacctaaacagTATGGCCGTCCACTTTATGGAGATGTTTTTGGTGTTCATCAACAAGATCAGCCTAATTATGAG

upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G31350.1 (Glycine max), 3'ss of exon 6
gtaagcatttttttttatctacattcttcttttttattatttctatgccatctactaacttttattttttt--cccgttcttatcgtttgtgt-tacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG
 ||   | ||||  | ||  | |   |   ||    |  | ||    ||   | |    ||| |  | |||   |  || || | || ||    || | |||||||  ||||| | |||||||||||||||||||| || |||||||| |||||||| || |||
-tatatacttttgctgataaaaaaaataaattaaagtgctctcccacccccttcccccttttcacctctttgatcactttttcttgtctgcacctaaacagTATGGCAGTCCACTTTATGGAGATGTTTTTGGTGTTCATCAACAAGACCAGCCTAATTATGAG

upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 2
----------gtaagcatttttttttatctacattcttcttttttattatttctatgccatctacta--acttttatttttttcccgttcttatcgt-ttgtgttacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG
           | | ||| |    | |||||  | |   ||||||  || |   ||  ||||||  |  | ||| |  || |     || |  | ||  |  |||| |||||||||||| |||||||||||||||||||||||||| ||||||||||| || || ||||| |||
gtgagttactttcatcatgtagactaatctatttacccttttttttgtactgaaatatcatctatcattattttcagattctgattattttatttgtacttcgttaaatagTATGGGCGACCATTGTATGGAGATGTTTTTGGTGTTCAGCAACAAGAACAACCAAACTATGAG

upper sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 3'ss of exon 10
---gtaagcatttttttttatctacattcttcttttttat-tatttctatgccatctactaacttttatttttttcccgttcttatcgtttgtgttacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG
   ||  |  |     |  |  |   || |   |||| || ||||||||| |  |  | |     |  | |||  ||  ||  ||||  | | | | ||  ||||||||| || |||||||||||||| |||||||| |||||    || |    || ||  |||
tgagtctggttggcaatacagttgtgttatagattttcatctatttctatacgctgaaattgggatcttgtttaaccaattagtatctgtggggctgca--gTATGGGCGACCCTTGTATGGAGATGTATTTGGTGTTCAGCACGTGGAGCTTGATACCTTTGAG

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|125225911|gb|EL239996.1|EL239996
EST:     GCTGGCGGCTGGGGGAAACCTCCAGTTGACGAA                         TATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAA
genomic: GCTGGCGGCTGGGGGAAACCTCCAGTTGACGAAgtaagcattt ... tgttacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAA
EST: gi|164011717|gb|ES056646.1|ES056646
EST:     CTAGCTTTGGTTTTCATGCTGGCGGCTGGGG-AAACCTCCAGTTGACGAA                         TATGGGCGTCCA
genomic: CTAGCTTTGGTTTTCATGCTGGCGGCTGGGGGAAACCTCCAGTTGACGAAgtaagcattt ... tgttacatagTATGGGCGTCCA
EST: gi|164165211|gb|ES148298.1|ES148298
EST:     CTAGCTTTGGTTTTCATGCTGGCGGCTGGGGGAAACCTCCAGTTGACGAA                         TATGGGCGTCCA
genomic: CTAGCTTTGGTTTTCATGCTGGCGGCTGGGGGAAACCTCCAGTTGACGAAgtaagcattt ... tgttacatagTATGGGCGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgccatctactaacttttatttttttcccgttcttatcgtttgtgttacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG
         tactaac  putative branch site (score: 0)
      atctactaacttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatttttttttatctacattcttcttttttattatttctatgccatctactaacttttatttttttcccgttcttatcgtttgtgttacatagTATGGGCGTCCATTGTATGGAGATGTTTTTGGTGTCCAGCAACAAGATCAGCCTAACTACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA