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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattataacttttttaacatgtctacaatttatttttctatattttttcataagggtctaatgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA

Basic information

species Glycine max
transcript GLYMA17G20610.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------------------aattataacttttttaacatgtctacaatttatttttctatatttt-ttcataagggtctaatgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
                                                                       |   || |    | || ||| |   | | |||      | || ||| |||   |||    | || | ||  |   | |   ||| || |  | || |  || |||| ||||| ||||| |||||||||||| | || || ||||| || || ||||||||||||||||||||  |||| || ||| | ||  |||||||||
gtactcatatatttgaatttacatgcttgcgtcctgaatatggtgtcatggtgtctcagtctggtatattgatacatcatacatgtaccattttctccacttaagcaattgtactttcttcgcgaggcatcagtgcgattgctgactaaatatttgtttc--tcaacaa-agATTGCTGATGTGTGGTCGTGTGGAGTAACCCTCTACGTAATGCTGGTTGGTGCATATCCTTTTGAGGATCCAGATGAGCCTAAGAATTTCAGGAAGACAA

upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G066867_T01 (Zea mays), 3'ss of exon 5
----aattataacttttt-taacatgtctacaatttatttttctatattttttcataagggtctaatgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
    |   |    || |  | |  | | |  |    |     |||| ||      |  |   |  |||    ||      ||  | ||| |  | | || |  || | || ||||| |||||||||||||||||  | || |||||||| || || |||||||| |||||||| ||  |||| || ||| | ||  |||||||||
atacacgcacggtttgtagtcatgtatatgtatagcaggaaactatgttggcaagttggaaccctatg----tcagtcactaactcttcgt-tactgaaaacaagGTCGCTGATGTGTGGTCATGTGGAGTAACGCTGTACGTGATGCTGGTCGGTGCATATCCATTTGAGGACCCAGATGAGCCTAAGAATTTCAGGAAGACAA

upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 6
-aattataacttttttaacatgtctacaatttatttttctatattttttcataagggtctaatgggttt--cttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
   || | | | |  |    ||||| | |   |      | | |  ||   |||   |  || |  |     ||||| | ||  || || ||   ||| | || ||||||| || ||||||||||| ||||| |||||||| ||||| || || ||||||||||||||||||||| ||||||| |||||||| || || ||||
agttttttattctgcttgagtgtcttccagacacacag-tgtttcattatctaattattcaaagaatcaaatttctggtttgactt-ttacaaa-aatttcagATTGCAGACGTGTGGTCATGTGGGGTAACATTATATGTTATGCTTGTTGGTGCATATCCTTTTGAGGATCCTGATGAACCCAAGGACTTCCGAAAAACAA

upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 6
lower sequence: PP1S240_91V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------aattataacttttttaacatgtctac--aatttatttttctat----atttttt----cataagggtctaa----tgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
                                   | ||    ||| |   || ||| |  |  | | | | ||||    |||||||    |||  ||    ||    |  |     |  | ||||  | |||    | |||   || |||| ||||| ||||| |||||||| ||||| || |||||| ||||||| |||||||| |||||||||||  |||| |||| | | ||  |||| || |
gtatgctgctcagacgaggattcgtttttgtgaggtgattggatttctggtatctctgcggagctcagtgtactatcgaaattttttagggcatgtggcatcaagttatcagggaactgagatatgcctacttcttgtgaatcgcagATTGCCGATGTGTGGTCGTGTGGAGTGACCTTGTACGTGATGTTAGTGGGGGCATATCCGTTTGAGGATCCCGATGACCCAAGGAATTTCAGGAAAACCA

upper sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 6
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------aattataactttttta-acatgtctacaatttatttttctatattttttcataagggtctaatgggtttcttctgttat----gttttcttgcatttaatat-tagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
                                                  |  ||    || | |  |    ||  |  |  ||||  | |   |     ||   ||  |  |   ||  || | ||     | |   ||||   | ||||  || |||||||||| ||||| || || || ||||| || |||||| | || |||||||||||||| ||||||||| | || |||| | | ||  |||| || |
gtaagtttttcggaagcgtgttggttttagtggaataaattggttcttggacaatgctattatcatgcggaactgaagctatttttggtgtcggtgaggttacaagtgcacggctctttgtcagctaaagaggctgatttgc-cgtgatatacagATTGCAGATGTGTGGTCTTGCGGTGTTACCTTGTACGTGATGTTGGTTGGAGCATATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCA

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|26046047|gb|CA783394.1|CA783394
EST:     CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG                         CTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
genomic: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtt ... ttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
EST: gi|18714643|gb|BM522792.1|BM522792
EST:     CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG                         CTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
genomic: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtt ... ttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
EST: gi|15662107|gb|BI699478.1|BI699478
EST:     CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG                         CTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
genomic: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtt ... ttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
EST: gi|254320505|gb|GR826954.1|GR826954
EST:     CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG                         CTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
genomic: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtt ... ttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
EST: gi|20811762|gb|BQ296240.1|BQ296240
EST:     CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG                         CTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
genomic: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtt ... ttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
EST: gi|254342837|gb|GR858999.1|GR858999
EST:     CTGCATATA-TGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG                         CTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
genomic: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtt ... ttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
EST: gi|120533008|gb|EH261141.1|EH261141
EST:     CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG                         CTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA
genomic: CTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAGgtagagtgtt ... ttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcataagggtctaatgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA
                                       ttgcatttaatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattataacttttttaacatgtctacaatttatttttctatattttttcataagggtctaatgggtttcttctgttatgttttcttgcatttaatattagCTTGCAGATGTCTGGTCATGTGGAGTAACCTTATATGTGATGCTAGTGGGAGCATATCCTTTTGAGGATCCTAATGAACCAAAGGACTTTCGGAAGACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA