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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgttacactttgtcaatgagaaaaagtgaatctgtttttgctgtgtcaacatgacaaccctaaatcattttaatttttacacattttagcatttcagttttcagctgtgtatttaacgtgaaatctcattgttgtgatggatttacctatagCTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCAATGACAACATTGTCTCTTGAAGCTCGCGAAAAACTTTCCAAG

Basic information

species Glycine max
transcript GLYMA08G00380.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g72980.2 (Oryza sativa), 3'ss of exon 11
gtatttgttacactttgtcaatgagaaaaagtgaatctgtttttgctgtgtcaacatgacaaccctaaatcattttaatttttacacattttagcatttcagttttcagctgtgtatttaacgtgaaatctcattgttgtgatggatttacctatagCTGGTTGCAAAACA---ACATAGACCACTTCCTGAAGACTTGGATTACTATGCAATGACAACATTGTCTCTTGAAGCTCGCGAAAAACTTTCCAAG
                                                          | ||  || |     ||| || ||      ||| | ||  ||   |||   ||   ||    |  ||    | | | ||| | ||   |||  ||  | | | ||| ||| ||    || |     |||||||||||||| |||||  || |||||||||   |||| ||||||||||| || |||||||| |||
----------------------------------------------------------agaattctgatgttgtttcatattcctttgttt-aacacctcttgttttttctacctagaagatatgctgacccctcgtttt-atttttttctcttcatcagATTGTAAATCAGGAGCACAAGAAGCTTCCTGAAGACTTAGATTATCATTCAATGACAAACCTGTCACTTGAAGCTCGTGAGAAACTTTCAAAG

upper sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G481548_T01 (Zea mays), 3'ss of exon 11
----gtatttgttacactttgt--caatgagaaaaagtgaatctgtttttg---ctgtgtcaacatgacaac----cctaaatcattttaattttt--------acacatttt--agcatttca--------gttttcagctgtgtatttaacgtgaaatctcattgttgtgatg---gatttacctatagCT---GGTTGCAAAACAA---CATAGACCACTTCCTGAAGACTTGGATTACTATGCAATGACAACATTGTCTCTTGAAGCTCGCGAAAAACTTTCCAAG
     |  || |     | ||    | ||  |   |||  || |    | |   |||       |  ||||     | | |||| ||  |  | |          |||||| |  |  ||||||        |||||    ||| || || |   |  | || | | ||||| ||   | |||  || |   |   | | | ||| |||   || ||   |||||||||||| ||||||||| |  |||||||||   | || ||||||||||| || ||||||||||||
gtaattgcttatggggttatgcgatagtgttatggagtagatttacgatggaagctgaactgctagaacaatggtacatgaatcgttcgagatgtccaacagtagcacattatgcatgatttcatttgttttgttttgttttgtttaattgataaggcagctaacttttgtgttgtttgttttctctctttgttaagATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG

upper sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 10
lower sequence: AT2G13440.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatttgttacactttgtcaatgagaaaaagtgaatctgtttttgctgtgtcaacatgacaaccctaaatcattttaatttttacacattttagcatttcagttttcagctgtgtatttaacgtgaaatctcattgttgtgatggatttacctatagCTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCAATGACAACATTGTCTCTTGAAGCTCGCGAAAAACTTTCCAAG
                                                             | | |   | |  || |||  | ||     ||  | ||   |  || | | | |     || || | |   |     || ||    |||   |||| ||||     |||||||||||| |||||| || || |||||||||||| | ||||||||  | || | |||||  || ||||||||||| |||
-----------------------------------------------------------gtatcttgtgttagcttcattactccattaaatactacttgcttactcggatatatg---gacatggagttataa----gttatatcctta---atagATGGTCCACCAACAACATAGACGACTTCCAGACGATTTGGATTACTATTCGATGACAACTCTATCCCATGAAGGGCGTGAAAAACTTTCAAAG

upper sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv04s0044g01690.t01 (Vitis vinifera), 3'ss of exon 11
gtatttgttacactttgtcaatgagaaaaagtgaatctgtttttgctgtgtcaacatgacaaccctaaatcattttaatttttacacattttagcatttcagttttcagctgtgtatttaacgtgaaatctcattgttgtgatggatttacctatagCTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCAATGACAACATTGTCTCTTGAAGCTCGCGAAAAACTTTCCAAG
                || |||||   | | |   ||  || ||||  |          ||   |  | | |   |||||| | ||  | | |   | |  |  |  |  ||| | |||||   |  ||    || |  | || |   ||  | ||| ||| |    | ||||| |||||||| || || |||||||||||||||||||||||||| ||||||||||| ||||| || ||||| ||||||
----------------gtgaatgatccatatttggtcacttattgccttt---------catttcctatttagaataatttgt-catgtctaaatttctgggcatatacttgtctgtttaatccgtcatagatttttccttattg---tatttgtagATGGCTCGTCAGCAACACAGACCACTACCAGAGGACTTGGATTACTATGCAATGACAACTTTGTCTCTTGAGGCTCGTGAGAAACTATCCAAG

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|254336022|gb|GR841347.1|GR841347
EST:     GTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAG                         CTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCA
genomic: GTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAGgtatttgtta ... ttacctatagCTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCA
EST: gi|5760607|gb|AI965970.1|AI965970
EST:     ATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAG                         CTGGTTGCAAAACAACATAGACCACT
genomic: ATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAGgtatttgtta ... ttacctatagCTGGTTGCAAAACAACATAGACCACT
EST: gi|7639325|gb|AW733650.1|AW733650
EST:     ATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAG                         CTGGTTGCAAAACAAC
genomic: ATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAGgtatttgtta ... ttacctatagCTGGTTGCAAAACAAC
EST: gi|14990848|gb|BI316521.1|BI316521
EST:     ATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAG                         CTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCA
genomic: ATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAGgtatttgtta ... ttacctatagCTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCA
EST: gi|21638885|gb|BM139931.1|BM139931
EST:     ATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAG                         CTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCA
genomic: ATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAGgtatttgtta ... ttacctatagCTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCA
EST: gi|16342700|gb|BI968295.1|BI968295
EST:     ATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAG                         CTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCA
genomic: ATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAGgtatttgtta ... ttacctatagCTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcagctgtgtatttaacgtgaaatctcattgttgtgatggatttacctatagCTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCAATGACAACATTGTCTCTTGAAGCTCGCGAAAAACTTTCCAAG
             atttaac  putative branch site (score: 3)
                                            tttacct  putative PPT
          tgtatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgttacactttgtcaatgagaaaaagtgaatctgtttttgctgtgtcaacatgacaaccctaaatcattttaatttttacacattttagcatttcagttttcagctgtgtatttaacgtgaaatctcattgttgtgatggatttacctatagCTGGTTGCAAAACAACATAGACCACTTCCTGAAGACTTGGATTACTATGCAATGACAACATTGTCTCTTGAAGCTCGCGAAAAACTTTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC