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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcacaatatggttcttctctcatgcaattcttttattaatcccatttcagcataatgagccatatttgtttttgatgattcttctttctacattcatagGATATTACCTTACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAATGGGATTTTTAGGATCTGTTATTCTCTCATTTTCCTTCTCTATGTTTAA

Basic information

species Glycine max
transcript GLYMA16G15800.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G15800.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g32830.1 (Oryza sativa), 3'ss of exon 2
tgcacaatatggttcttctctcatgcaattcttttattaatcccatttcagcataatgagccatatttgtttttgatgattcttctttctacattcatagGATATTACCTTACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAATGGGATTTTTAGGATCTGTTATTCTCTCATTTTCCTTCTCTATGTTTAA
                  |   |  | |  |  | || |||     |  |        ||   |      || |||      ||  || || |||   |||  ||||||| ||||||||  |||| |||||||||||||||||| |  | ||||||||| | || || || ||  | || ||| | ||||| ||||| ||
-----------------gttgtaaactaaaccctgatcaatagtgctctaat----caagttgtg---aattctgaaataagttggtttta-attgccagGTGATTACCTCACAAAGGCGCCATCTAATCCTGGAGCTGGTGACGTCCTGATGGGATTTCTTGGTTCAGTCATCATATCGTTTGCATTCTCAATGTTCAA

upper sequence: GLYMA16G15800.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 4
tgcacaatatggttcttctctcatgcaattcttttattaatcccatttcagcataa--tgagccatatttgt-ttttgatgattcttctttctacattcatagGATATTACCTTACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAATGGGATTTTTAGGATCTGTTATTCTCTCATTTTCCTTCTCTATGTTTAA
 | | | | |   |   || | |   ||    |  |  || ||  |||   | |||         ||   |  ||||| | | |  |||||  |   | | |||| | |||||||| || | | ||||| ||||||| ||||||||||| |||||||| ||| | || ||||| |||||||| ||  | ||||| ||||| ||
-gtaaagt-taccttcactatgaaagaaactatagagaaacccttttttgacctaaaacagaaagtaaaagcattttgttaactgctcttta-atggtgacagGAAACTACCTTACCAAAGTAGCATCAGATCCTGGTGCTGGTGACATCTTAATGGGTTTTCTTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAA

upper sequence: GLYMA16G15800.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0056g01690.t01 (Vitis vinifera), 3'ss of exon 4
---tgcacaatatggttcttctctcatgcaattcttttattaatcccatttcagcataatg---agccatatttgtttttgatgattcttctttctacattcatagGATATTACCTTACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAATGGGATTTTTAGGATCTGTTATTCTCTCATTTTCCTTCTCTATGTTTAA
   | |     ||  || ||      ||  ||| || | |||||      |   |||| |       | ||| | | |||  | |||||||| |  | ||  ||||||||||||||||| |||||||| || ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| | ||||| ||||| ||
gattcctttgcataattgtt------tggtatttttcttttaatttagaatatacatatttcttgctcgtatgtttatttattaattcttctgttaatatgaatagGATATTACCTTACGAAGGCATCTTCTAATCCTGGAGCTGGTGACATTCTAATGGGATTTTTAGGATCTGTTATTCTCTCATTTGCTTTCTCCATGTTCAA

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|207770400|gb|GD744142.1|GD744142
EST:     AGCATTTGCTTTTGGGTATTTTTCCAAGTCAGGACTTGAACCTGTGCTAG                         GATATTACCTTACAAAGGCATCATCAAATCCTGGAG
genomic: AGCATTTGCTTTTGGGTATTTTTCCAAGTCAGGACTTGAACCTGTGCTAGgtatggttaa ... acattcatagGATATTACCTTACAAAGGCATCATCAAATCCTGGAG
EST: gi|51337909|gb|CO981775.1|CO981775
EST:     AGCANNTGCTTTTGGGTATTTTTCCAAGTCAGGACTTGAACCTGTGCTAG                         GATATTACCTTACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAA
genomic: AGCATTTGCTTTTGGGTATTTTTCCAAGTCAGGACTTGAACCTGTGCTAGgtatggttaa ... acattcatagGATATTACCTTACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAA
EST: gi|151403336|gb|EV273146.1|EV273146
EST:     AGCATTTGCTTTTGGGTATTTTTCCAAGTCAGGACTTGAACCTGTGCTAG                         GATATTACCTTACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAA
genomic: AGCATTTGCTTTTGGGTATTTTTCCAAGTCAGGACTTGAACCTGTGCTAGgtatggttaa ... acattcatagGATATTACCTTACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagcataatgagccatatttgtttttgatgattcttctttctacattcatagGATATTACCTTACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAATGGGATTTTTAGGATCTGTTATTCTCTCATTTTCCTTCTCTATGTTTAA
                         ttttgat  putative branch site (score: 4)
                                  ttcttctttctacatt  putative PPT
                 atatttgtttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcacaatatggttcttctctcatgcaattcttttattaatcccatttcagcataatgagccatatttgtttttgatgattcttctttctacattcatagGATATTACCTTACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAATGGGATTTTTAGGATCTGTTATTCTCTCATTTTCCTTCTCTATGTTTAA

tgcacaa
- - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - ccatttc