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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcaaattgtttcaaaaacattacattgacacttcttatacattacactaactccgcttaactgctaattctaacttctttttcctctccttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTGATGAAGTGGCTGATATCAAATATGTGAACCGTGATCAGTTGAAGGAGCT

Basic information

species Glycine max
transcript GLYMA09G38550.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 3'ss of exon 5
ctcaaattgtttcaaaaacattaca-ttgacacttcttatacattacactaactccgcttaactgctaattctaacttctttttcct---ctccttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTGATGAAGTGGCTGATATCAAATATGTGAACCGTGATCAGTTGAAGGAGCT
    | | | ||    | |    |  || | ||| |   |   | |   |  || |  ||||||  ||||  | ||   ||||||||   ||||   ||| |||| || ||||| || ||||||||||| |||||||||||||| || || ||||||||||| |||||| | || ||||||  |||  || |  |||| |||||
--tcattagcttagccagctgcccggtttatactgccagt-tgtgagtgtttctacctttaacta-taatgttgacccttttttccttatctccacaattacagTTGATTATCTACTCTTCATTGTCCGAGATGTTAATGTGAATCCAAACCCTGATGAAGTTGCTGATGTTAAGTATGTGTCCCGGAATGATCTGAAAGAGCT
















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|6848648|gb|AW350938.1|AW350938
EST:     TCGCATTCTTTACAAGGCANNNNCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
EST: gi|17022222|gb|BM093256.1|BM093256
EST:     TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAAT
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAAT
EST: gi|193552359|gb|FK508990.1|FK508990
EST:     TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
EST: gi|26268343|gb|CA819406.1|CA819406
EST:     TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
EST: gi|13563422|gb|BG551651.1|BG551651
EST:     TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
EST: gi|38191106|gb|CF920312.1|CF920312
EST:     TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
EST: gi|31468516|gb|CD410544.1|CD410544
EST:     TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCNATCCTG
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
EST: gi|9259122|gb|BE347269.1|BE347269
EST:     TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
EST: gi|8283037|gb|BE020598.1|BE020598
EST:     TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTNTTCATTGTCCGGGATGTT
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTT
EST: gi|24136754|gb|BU927264.1|BU927264
EST:     AGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
genomic: AGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
EST: gi|15813110|gb|BI785385.1|BI785385
EST:     TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
EST: gi|19938293|gb|BQ081652.1|BQ081652
EST:     TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAAC                         TGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG
genomic: TCGCATTCTTTACAAGGCACCTTCTGATGGCAAATGGGGAGAGCATGAACgtaagccaat ... ttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactaactccgcttaactgctaattctaacttctttttcctctccttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTGATGAAGTGGCTGATATCAAATATGTGAACCGTGATCAGTTGAAGGAGCT
                   ctaattctaacttctt  CT-rich tract
                    taattctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcaaattgtttcaaaaacattacattgacacttcttatacattacactaactccgcttaactgctaattctaacttctttttcctctccttgattgcagTGGACTATCTGCTTTTCATTGTCCGGGATGTTAATGTGAACCCCAATCCTGATGAAGTGGCTGATATCAAATATGTGAACCGTGATCAGTTGAAGGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - -aaaaaca
- - - - - - - - - - - - - tgacact
- - - - - - - - - - - - - - - - - - - - - - -cactaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgcta