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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatccttttaaaaagtaactttttattttattttgaagccagcaataaccaaatagtttgaacacgaacaatacattctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG

Basic information

species Arabidopsis thaliana
transcript AT1G79500.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79500.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 10
------------------gtatgatccttttaaaaagtaactttttattttattttgaagccagcaataaccaaatagtttgaacacgaacaatacattctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG
                   ||   ||| ||    || || || | |||||    |  |||    |  |   ||||| ||     ||       | |  | |  |  || | |||||||| |||||||||||||| ||| | || ||  ||||||||||||| ||||| ||  |||| || || || || ||||| ||||||||||||
agttttttgaacaccatgttaccgtcccttcctcaaatatctatgtatttg---tgcaagtagacggttgtcaaattgt----gcatatttggttctcttttgta-agCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG

upper sequence: AT1G79500.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 3
gtatgatcct--tttaaaaagtaactttttat---tttatt-ttgaagccagcaataaccaaatagtttgaacacga----acaatacattctgatgta-gTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG
 | |  ||    ||| | || || ||| | ||   |||||| |||       |  |       |   || ||   |      |  |   || |  |||| | | |||||||| ||||||||||| || || || || ||  ||||||| ||||||||||| ||  |||| || ||||| || ||||| ||||||||||||
-tttcgtcacaatttcagaactagcttatgatgaatttattgttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG

upper sequence: AT1G79500.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 9
------gtatgatcct---tttaaaaagtaactttttattttattttgaagccagcaataaccaaatagtttgaacacgaacaatacattctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG-
       | |  | ||   ||| |||| ||||||| |    |    |      | |    |||   |   ||| |    ||   | | |||     ||||||||||| || |||||||| |||||||| ||||| ||  ||||||| ||||||||||| ||||| || || ||||| || ||||| || ||||||||| 
tgacttctgtagttctagcttttaaaaataactttctgaaatgacctttccaaatcttacacctggttcattggattaaaattctgctttcatgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG

upper sequence: AT1G79500.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G38010.1 (Glycine max), 3'ss of exon 10
-------gtatgatcctt-ttaaaaagtaactttttattttattttgaagccagcaataaccaaatagtttgaacacgaacaatacattctgatgta--gTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG
        | |  | ||   |   || ||||||| |    |    |     || |    |||   |   |||||    ||   | | ||||  ||||  ||||||||| || ||||| ||||||||||| ||||| ||  | ||||| ||||||||||| ||||| || || ||||| || ||||| || |||||||||
ctgacttctgtagttctagcttttaaataactttctgaaatgacctttccacatcttacacctggttcgttgaattaaaattctgctttcttgtgtatagTTGGATGGAGGAGGTGTGGCAAGTGGAGGTCTTCGAGAACTGATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAG

upper sequence: AT1G79500.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 9
--------------gtatgatccttttaaaaagtaactttttattttattttgaagccagcaataaccaaatagtttgaacacgaacaatacattctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG
                || ||  ||||| |   | |      ||||| | || |    |  || |  |  ||  |    |    ||       || | |   || |||| || || |||||||| |||||||| ||||| || || |||||||||||||| || ||||| || || ||||| || ||||||||||||||||||
taaatttgaatgccacataata-ttttagatgctgag---ccattttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG

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|164190794|gb|ES045801.1|ES045801
EST:     GTCGCTGATATAACCCATTCACTACAATAACCTGCAGGCAAAGAAG                         TTGGATGGTGGTGGTGTTGCAAGTGGAGGCC
genomic: GTCGCTGATATAACCCATTCACTACAACAACCTGCAGGCAA-GAAGgtatgatcct ... tctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCC
EST: gi|309381091|gb|HO850312.1|HO850312
EST:     GTCGTTGATATAACCCATTCACTACAACAACCTGCAGGCAAGAAG                         TTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAG
genomic: GTCGCTGATATAACCCATTCACTACAACAACCTGCAGGCAAGAAGgtatgatcct ... tctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaagccagcaataaccaaatagtttgaacacgaacaatacattctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG
                   aaatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatccttttaaaaagtaactttttattttattttgaagccagcaataaccaaatagtttgaacacgaacaatacattctgatgtagTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA