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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcactcatcatccctatttttgcttcatgataaaacttgacttccatcatttatttctggattattgaatacccttctgatttgatttcaactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAAAATCTAAATGCCCTTGTTAAGGTTCTTCCTGGTCTACTTGGTGGCAGTG

Basic information

species Glycine max
transcript GLYMA20G38720.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 6
cttcactcatcatccctatttttgcttcatgataaaacttgacttccatcatttatttctggattattgaatacccttctgatttgatttcaactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAAAATCTAAATGCCCTTGTTAAGGTTCTTCCTGGTCTACTTGGTGGCAGTG
  | | || |  |  | |||| | ||     |||| | ||||  |     || |   |   ||   |  |||       | | |||||||  ||    ||| |||||||||||| |||||||| ||||| || || |||||||| |||||     |||| || |||| ||| ||| |||||||||| ||||| || ||||
-gtaagtctt--ttaccatttctactc----ataacatttgagct--ggtatgtgaatgatgacattctaatggtagatt-acttgatttgtac----agAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAGTGCTTAAACGCACTTGCTAAAGTTGTTCCTGGTCTTCTTGGAGGAAGTG

upper sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 6
------------------------cttcactcatcatccctatttttgcttcatgataaaacttgacttccatcattta-----tttctggattattgaatacccttctgatttgatttcaactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAAAATCTAAATGCCCTTGTTAAGGTTCTTCCTGGTCTACTTGGTGGCAGTG
                        |     ||||   |      ||| | | ||||| |   |  || | ||   |||      ||| | | || | | | | | || |  | ||  ||    | |||||| |||||||| |||||  ||||||||||||| |||||||||||||| |||  ||| ||||| || |  || ||||||||||| || || ||||||||||
gtgagtgatggatttccctaatcacggtgttcatggacttgcaattttcctaatgatgatcatgaacgtacaatttttgcactttttattgcttttagtaaaacgttattttctgtcttt--ttctcagACTTACACTCCTGAAAGTGCTGCTGATGCTACCAGAAATCTGTCTCAACAATGTCTTAATGCTCTGGCCAAAGTTCTTCCTGGGCTCCTAGGTGGCAGTG
















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|7283818|gb|AW596420.1|AW596420
EST:     AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCG                         ACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
genomic: AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCGgtgagtaaac ... caactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
EST: gi|27808938|gb|CB063360.1|CB063360
EST:     AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCG                         ACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
genomic: AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCGgtgagtaaac ... caactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
EST: gi|16279267|gb|BI943346.1|BI943346
EST:     AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCG                         ACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
genomic: AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCGgtgagtaaac ... caactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
EST: gi|16284081|gb|BI945895.1|BI945895
EST:     AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCG                         ACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
genomic: AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCGgtgagtaaac ... caactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
EST: gi|209722231|gb|BW651248.1|BW651248
EST:     AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCG                         ACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
genomic: AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCGgtgagtaaac ... caactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
EST: gi|7692105|gb|AW760220.1|AW760220
EST:     AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTNCG                         ACATACACTCCAGANAGCCCTGCTGATGCTANCA-GAAATCTGTCT
genomic: AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCGgtgagtaaac ... caactttcagACATACACTCCAGAAAGCCCTGCTGATGCTA-CAAGAAATCTGTCT
EST: gi|120532309|gb|EH260442.1|EH260442
EST:     AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCG                         ACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
genomic: AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCGgtgagtaaac ... caactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
EST: gi|17401949|gb|BM178731.1|BM178731
EST:     AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCG                         ACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA
genomic: AGGCTATTATTACTGGTGAATTACCAGCTGGTTGGGAGAAAGCACTTCCGgtgagtaaac ... caactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatcatttatttctggattattgaatacccttctgatttgatttcaactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAAAATCTAAATGCCCTTGTTAAGGTTCTTCCTGGTCTACTTGGTGGCAGTG
                                                ctttc  CT-rich tract
                 attattgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcactcatcatccctatttttgcttcatgataaaacttgacttccatcatttatttctggattattgaatacccttctgatttgatttcaactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAAAATCTAAATGCCCTTGTTAAGGTTCTTCCTGGTCTACTTGGTGGCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- tcactca
- - - - -tcatccc
- - - - - - - - - - - tgcttca
- - - - - - - - - - - - - - - gataaaac
- - - - - - - - - - - - - - - - - - - - - - tccatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttct