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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttgtgttttactgttttaggagtcagtgtattttaattgaattcacatgtttttctgaattggcaatgatatatatctacattttttgtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGGAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG

Basic information

species Glycine max
transcript GLYMA07G32190.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G32190.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 9
atgttgtgttttactgttttaggagtcagtgtattttaattgaattcacatgtttttctgaattgg--caatgatatatatctacattttttgtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGGAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG
   |  |  |||  |   | | ||     ||||||  |   |  |   ||     |  ||  |||    ||| | ||   | |     |||||    |  || | ||||||||||| |||||||||||||| |||||||| ||||||||||| |||||  |||||||||| ||||||||||| || || ||  | |||||||
--ttcctagtttcgtccctaatgacattatgtattcaataagggtcatcaaaaagtcatgtgttgagataataaaattattttctgccttttgaattctcagCTAGCTACCAACACCCTGGAGAGAGTGGCACCTCTCACACATGCAGTTGGCAACGTCTTGAAACGTGTTTTTGTGATTGGTTTCTCGATCTTGGTCTTTG
















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|11688177|gb|BF595853.1|BF595853
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|15204849|gb|BI427617.1|BI427617
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|23728678|gb|BU762399.1|BU762399
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|7691785|gb|AW759906.1|AW759906
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|14999814|gb|BI320628.1|BI320628
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|20449753|gb|BQ253877.1|BQ253877
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|15284741|gb|BI468632.1|BI468632
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|207826480|gb|GD798191.1|GD798191
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|31561027|gb|CD486865.1|CD486865
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|16346698|gb|BI972293.1|BI972293
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|15199917|gb|BI424075.1|BI424075
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|14011803|gb|BG726725.1|BG726725
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|20498205|gb|BQ273135.1|BQ273135
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGA
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGA
EST: gi|6481839|gb|AW201110.1|AW201110
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|26269373|gb|CA820436.1|CA820436
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|31475923|gb|CD417951.1|CD417951
EST:     TCGTCTCAGATCTCTTCTGGTTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCTACACACTGGAGAGATTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|10237564|gb|BE806452.1|BE806452
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
EST: gi|10232365|gb|BE801253.1|BE801253
EST:     TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAG                         GTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG
genomic: TCGTCTCAGATCTCTTCTGGGTTGGTATGTTTTACCATCTCTACAACCAGgtaaatccat ... gtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacatgtttttctgaattggcaatgatatatatctacattttttgtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGGAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG
                                       ttttttgtc  CT-rich tract
                      aatgatatatatctac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttgtgttttactgttttaggagtcagtgtattttaattgaattcacatgtttttctgaattggcaatgatatatatctacattttttgtcaccatagGTGGCTACCAACACACTGGAGAGAGTGGCTCCTCTCACTCATGCAGTTGGGAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG

-tgttgtg
- - - - - - - - - - - - - - - - - - - - - -attcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacatt