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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcttaaccaatctagcttatttgttttaattggatgttactcggattttttttttgtctattaattgtgttagcctattaatcatatgaattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGTGGGGTCACCAGGCCAGTGATTGCTTGTTCTGTGACAACTAATGAAGGGA

Basic information

species Glycine max
transcript GLYMA17G12430.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12430.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g03540.1 (Oryza sativa), 3'ss of exon 2
--aatctta-accaatctagcttatttgttttaattggatgttactcggattttttttttgtctattaattgtgttagcctattaatcatatgaattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGTGGGGTCACCAGGCCAGTGATTGCTTGTTCTGTGACAACTAATGAAGGGA
   | |||  | |   ||  |  |         | |||   | |  |        |||    ||   ||| ||||       | | |  ||   || |   |||||||||| ||||| |||||||| ||||| ||||| || || |||||||||||||| || ||||| ||||| || || || ||||| |  ||||| |  |
ttgaccttgcatctcactttcacacgcacgcccactggccataaaccatgaagagtttcatcct--caatggtgtaccgaactcatttgtaccgatgtgc-agAATGTGCCATACGTCTTTGTCCCATCAAAGCAAGCTCTCGGCCGTGCATGTGGGGTGACGAGGCCCGTGATCGCCTGCTCGGTGACCAGCAATGAGGCCA

upper sequence: GLYMA17G12430.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G22380.1 (Arabidopsis thaliana), 3'ss of exon 1
------aatcttaaccaatctagcttatttgtttta--attggatgttactcggattttttttttgtctattaattgtgttagcctattaatcatatgaattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGTGGGGTCACCAGGCCAGTGATTGCTTGTTCTGTGACAACTAATGAAGGGA
       ||| ||    | | |||||  ||  | ||  |     | ||||  || | |  ||||   |||    || | |     || |   ||| | |||     |||||||||| || |||||||| ||||| ||||||||| | ||| | |||||||| || || || || || ||||||||||| |||||| | ||||| |  |
atagtttatcctatttgaacaagcttcattactatacaagcaattattacgtgg-tctgattttgaactaacgcttttttg----tactctccatctaaatg---cagAATGTGCCATATGTGTTTGTACCTTCGAAACAAGCATTGGGAAGAGCATGTGGAGTAACAAGACCTGTTATTGCTTGTTCAGTGACATCGAATGAGGCAA

upper sequence: GLYMA17G12430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g05140.t01 (Vitis vinifera), 3'ss of exon 3
-----aatcttaaccaatctagcttatttgttttaattggatgttactcggattttttttttgtctattaattgtgttagcctattaatcatatgaattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGTGGGGTCACCAGGCCAGTGATTGCTTGTTCTGTGACAACTAATGAAGGGA
     ||  ||     |  ||  ||     ||||  ||   || || |      |  || |  |  ||| ||      ||     | ||  | |||||||   |||||||||| || || |||||||||||||| ||||||||||| ||||||||||| ||||| ||||| || ||||| ||||| ||||| |  ||||| || |
gttgaaacatttttatagatattttcagaattttgtttccttgctagttcagaataattataatgcattcataaca--agttc--tgattct-tgaatttggcagAATGTGCCTTATGTATTTGTCCCTTCAAAGCAAGCACTTGGCCGTGCATGTGGAGTCACAAGGCCTGTCATTGCCTGTTCGGTGACTAGCAATGAGGGAA

upper sequence: GLYMA17G12430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g02650.t01 (Vitis vinifera), 3'ss of exon 3
aatcttaaccaatctagcttatttgttttaattgga--tgttactcggattttttttttgtctattaattgtgttagcctattaatcatatgaatttttt-----agAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGTGGGGTCACCAGGCCAGTGATTGCTTGTTCTGTGACAACTAATGAAGGGA
    |     |    || | | | || | ||||| |    | | | |        |||  |  | |  || ||  | || ||| |   | | |||||  |     ||||||||||||| || ||||| ||||||||||||||||||||||| |||||||| ||||| |||||||||||||||||||||||||| |  || ||||| |
----taggatatggaagttaaatggtgtgaattgtagccatgaattgagaacaaatttctttcact--ttctggaaaccaattcacttt-taaatttcctgtggcagAATGTGCCCTATGTATTTGTACCTTCAAAACAAGCACTTGGACGAGCATGTGGAGTCACAAGGCCAGTGATTGCTTGTTCTGTGACGAGCAACGAAGGAA

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|298182539|gb|HO031274.1|HO031274
EST:     CTGAGCCCCTTGAGATTCTTCTACATCCTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|298180380|gb|HO025581.1|HO025581
EST:     CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|6725768|gb|AW310167.1|AW310167
EST:     CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|298185053|gb|HO030266.1|HO030266
EST:     CTGAGCCCCTTGAGATTCTTCTACATCCTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|298171220|gb|HO016252.1|HO016252
EST:     CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|298195944|gb|HO044335.1|HO044335
EST:     CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|6566245|gb|AW233926.1|AW233926
EST:     CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|193711701|gb|FK648290.1|FK648290
EST:     AGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: AGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|26059372|gb|CA802286.1|CA802286
EST:     CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|298189335|gb|HO037738.1|HO037738
EST:     CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|18039291|gb|BM307585.1|BM307585
EST:     CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
EST: gi|298164419|gb|HO014064.1|HO014064
EST:     CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAG                         AATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT
genomic: CTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGATAAGgtatgctaat ... aattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttttttttgtctattaattgtgttagcctattaatcatatgaattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGTGGGGTCACCAGGCCAGTGATTGCTTGTTCTGTGACAACTAATGAAGGGA
                                tattaat  putative branch site (score: 2)
                                               tttttt  putative PPT
                                tattaatcatatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcttaaccaatctagcttatttgttttaattggatgttactcggattttttttttgtctattaattgtgttagcctattaatcatatgaattttttagAATGTGCCCTACGTGTTTGTCCCTTCAAAACAAGCACTTGGACGTGCATGTGGGGTCACCAGGCCAGTGATTGCTTGTTCTGTGACAACTAATGAAGGGA

- - - - - - - - - - - - - - - - tggatgt