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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttcacaacaatttatgcacgtactatcatctgaattctgatcaatataatttgtttagcatttttgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG

Basic information

species Glycine max
transcript GLYMA13G20790.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
gtaaatttcacaacaatttatgcacgtactatcatctgaattctgatcaatataatttgtttagcatt-tttgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
|||| | | || || | | |||| | || | | || ||| | | | | ||| | ||||||||||| ||||| || ||||| | ||||| || || || |||||||||||||| || || ||||||||||| |||||||||||| | |||| | |
gtaagcattcttaaaagcaatat---cattttcattggtcttgttagcattattcatcactgtgtgctatttattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG

upper sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 3
gtaa--atttcacaacaatttatgcacgtactatcatctgaattctgatcaatataatttgtttagcatttttgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
|||| ||| || | | ||| | ||| || | |||| | | | || | | || ||||||||||||||||||| || |||||| | ||||| |||||||| ||||||||||| || || || ||||||||||| || ||||||||||| |||| | |
gtaagcattcttaaagagatgttgcttcaattattgtc---accatgattctttt--tcaccttgtcttaattccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGTTTGAGAGTGGCAGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGG

upper sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 3
gtaa--atttcacaacaatttatgcacgtactatcatctgaattctgatcaatataatttgtt----tagcatttttgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
|||| ||| || | | ||| | ||| || | || | | || || ||| | | | | || | | ||||||||||||||||| ||||||||| | ||||| ||||| || ||||||||||| || || || || ||||||||||| ||||||||||| |||| | |
gtaagcattcttaaagagatgttgcttcaattattgtcagt-ttgtcagcatgattctttttcaccctgtcctagtttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGTTTGAGAGTGGCAGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGG

upper sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 2
------------gtaaatttcacaa-caatttatgcacgtactatcatctgaattctgatcaatataat----ttgtttagcatttttgggttt--cagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
||| | | | | | | | || || || ||| | |||| || || |||||| | | | | ||||||| |||||||| || |||||||| ||||||||||| ||||| || ||||| || || || ||||||||||||| |||||||||| ||||||||||||
gtttagtttgttttaagtctattgatcgaatatttcaggttagttcttctaataaatgattctaatgatggttttgttttctcctgacgcatataatagGTTGTTAGAGGTGTGGTGGAAAGTCTTAAAATCATTACCCGTCAGGCGAGTTTGAGAGTTGCAGAGTATGCTTTTCTCTATGCCAAGACTCATGGAAGAG

upper sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 2
----gtaaatttcacaacaattta-tgcacgtactatcat--ctgaattctgatcaatataatttgtttagcatttttgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
|| ||||| | ||||| ||| | | | | || ||| | | ||| | | ||| | |||| | ||||| ||| |||||||||| ||||| |||||||| ||||| ||||| || ||||| ||||| ||||||||||| ||||||||||||||| | ||||||||||
gtgagttgttttcaagaggatttaatgctcatctgacaaatacttaatgcatagaaatttgaaggatttcttgtaattgg-tgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG

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|213607679|gb|DB958698.1|DB958698
EST:     TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|254321136|gb|GR827585.1|GR827585
EST:     TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|24135690|gb|BU926200.1|BU926200
EST:     TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|19348449|gb|BM892981.1|BM892981
EST:     TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAN                         GTTGTGAGAGGTGTA
genomic: TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtttcagGTTGTGAGAGGTGTA
EST: gi|209702312|gb|BW667500.1|BW667500
EST:     TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
genomic: TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGT
EST: gi|298197822|gb|HO039361.1|HO039361
EST:     TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTAGT
genomic: TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtttcagGTTGTGAGAGGTGTAGT
EST: gi|193453771|gb|FK421143.1|FK421143
EST:     TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAG                         GTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGT
genomic: TCACAATTCGTGAAAATACGGAAGGCGAGTACAGTGGACTTGAACATCAGgtaaatttca ... tgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactatcatctgaattctgatcaatataatttgtttagcatttttgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG
               ttctgat  putative branch site (score: 3)
 cattttt  putative PPT
 aatataatttgtttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttcacaacaatttatgcacgtactatcatctgaattctgatcaatataatttgtttagcatttttgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA