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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataacttttttttttttgtatgacccgtataattaaatattttccttttcctggtgctactatttcaatttttctattgaactaaattcaaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAG

Basic information

species Glycine max
transcript GLYMA11G35600.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G35600.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0067g01710.t01 (Vitis vinifera), 3'ss of exon 1
--aataacttttttttttttgtatgacccgtataattaaatattttccttttcctggtgctactatttcaatttttctattga---actaaattcaaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAG
  |  |      |    |   ||    | ||     |  |  ||||  || |        |  ||||| |  |||  |  |||    | ||  ||  ||   |||||  | || || ||| | ||||||||||| || || |||||||||||||||||||||
ttatcattcacataaaatacctactggctgtggcgctggaatttttgtttgtttc----ttcatatttaagatttgttgatgatatgcaaatgtcttata-acagGATTTATACATCCACGTCGGATGGCCTTTATACCGAAAATATGGTCATGCTTTTGAG
















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|6070400|gb|AW099787.1|AW099787
EST:     TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAG                         GAACTGTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
genomic: TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAGgtactaattg ... aaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
EST: gi|193623725|gb|FK575537.1|FK575537
EST:     TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAG                         GAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
genomic: TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAGgtactaattg ... aaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
EST: gi|151396190|gb|EV266067.1|EV266067
EST:     TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAG                         GAACTTTATATTCACATTGGATGGTCTTTGTATCGCAAATATGGTCATGCT
genomic: TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAGgtactaattg ... aaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
EST: gi|7284298|gb|AW596892.1|AW596892
EST:     TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAG                         GAACTNTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
genomic: TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAGgtactaattg ... aaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
EST: gi|298190105|gb|HO032226.1|HO032226
EST:     TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAG                         GAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
genomic: TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAGgtactaattg ... aaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
EST: gi|254323854|gb|GR840387.1|GR840387
EST:     TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAG                         GAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
genomic: TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAGgtactaattg ... aaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
EST: gi|192306825|gb|FK002995.1|FK002995
EST:     TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAG                         GAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT
genomic: TCCACTCCATCATGCGCCACGTCGCCGAAACCCTCAACATCGATTTGGAGgtactaattg ... aaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcctggtgctactatttcaatttttctattgaactaaattcaaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAG
                                   aactaaa  putative branch site (score: 2)
                tatttcaatttttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataacttttttttttttgtatgacccgtataattaaatattttccttttcctggtgctactatttcaatttttctattgaactaaattcaaatgtgcagGAACTTTATATTCACATTGGATGGCCTTTGTATCGCAAATATGGTCATGCTTTTGAG

- - - - - - - - - - atgaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gctacta