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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaccattctaatttcgttattatattgaaacaaacatatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCATC

Basic information

species Glycine max
transcript GLYMA07G01860.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 22
lower sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
gtgagtaccattctaatttcgttattatattgaaacaaacatatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCATC-
||||||    ||   ||       ||   |||||      ||   |     ||     |  ||  |||   |  ||   |  ||    |||||||  ||||| ||||||||| | ||||| |||||| |||| ||| |||||||||||||||||||  | || ||  | || ||| ||||  ||||  |  ||| 
gtgagttttcttg-gatcaaaccgtttctttgaactttttattcttcttggaag----atcaaagtaatggtgttattcatgttt-tatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAA-ATCA

upper sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
gtgagtaccattctaatttcgttattatattgaaacaaacatatcttac-ataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCATC
|| |||    |  | | | |    |||   |||  |     | |   |  | ||    | || |  |   | ||   | |   ||    ||||||| |||||||| ||||||| | ||||| ||||||||||| ||| |||||||||||||||||||  | || ||  | |||||  ||||  |  | ||||   
gttagttgtttcttcaat-cacctttaccgtgatccttttctgtaggattaaaaataatgcttatgttgttttttctctattctta---tttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA

upper sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G029506_T01 (Zea mays), 3'ss of exon 21
gtgagt-accattctaatttcgttattatattgaaacaaacatatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCATC
|| |||     ||  |||  |   ||      ||  |        | |  |  ||       |  |    | || |  |    ||    ||||||| |||||||  ||||||| | ||||| ||||||||||| ||| |||||||||||||||||||  | || ||  | |||||  ||||  | || ||||   
gtcagttgttgtttcaat--caccatccctgcgatccttttcctacctgtaggattaaatagaggactcatgttttttctctattcctgtttcagAGAATTCCTGGATGGTGGATCTGGTACTACTGGATTTGCCCACTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGGAAGACCTCA

upper sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 22
lower sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 18
gtgagtaccattctaatttc--gttattatattgaaacaaacatatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCATC
|| |||     |    ||||  |  |  |   ||||||    | ||  | |   ||   | ||| |||||      |    |||||    || |||| |||||| ||||||||| | |||||||||||||| ||||||||||| ||||| ||||||||||| ||||| || || ||  | ||  | |||||     
gttagtgttggttacttttctggcaagaaagctgaaaccc-taaatgattctctattgattctatcataagctggtt--ttactttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA

upper sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv09s0002g03570.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtaccattct---aatttcgttattatattgaaaca----aacatatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGAC-CATC
|| ||| |  ||     | |  | |    |  || |  |     |||  | || |   | |    ||||||  ||  || |    |  |||    |||||||||||||| || |||||| | ||||| || |||||||| ||| | ||||||||||| || ||  | || || || |||||| ||||  | |||||| ||  
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCACTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA-

upper sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv09s0002g03640.t01 (Vitis vinifera), 3'ss of exon 20
gtgagtaccattct---aatttcgttattatattgaaaca----aacatatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGAC-CATC
|| ||| |  ||     | |  | |    |  || |  |     |||  | || |   | |    ||||||  ||  || |    |  |||    |||||||||||||| || |||||| | ||||| || |||||||| ||||| ||||||||||| || ||  | || || || |||||| ||||  | |||||| ||  
gtaagttcattttcctcagtggcatagccactttcatgccttccaaccaacctcatccactacaaactaactcaaacctccattaatgtttaaaatttcagAAAATTCCCAAGTGGTGGATCTGGTACTATTGGATTTGCCCAGTAGCATGGACAGTTTACGGGCTGATCGTATCGCAATATGGAGACTTGGAGGACACAA-

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|13562742|gb|BG550962.1|BG550962
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAANTGGTGGGTGTGGTATTACTGGGATTTGTCCAGTGGCAT
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAA-TGGTGGGTGTGGTATTACTGG-ATTTGTCCAGTGGCAT
EST: gi|151406392|gb|EV276207.1|EV276207
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|16346225|gb|BI971820.1|BI971820
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|19938200|gb|BQ081608.1|BQ081608
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|151401523|gb|EV271337.1|EV271337
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|14205882|gb|BG839560.1|BG839560
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|16995911|gb|BM085283.1|BM085283
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|16343639|gb|BI969234.1|BI969234
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|15812818|gb|BI785093.1|BI785093
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|192328785|gb|FK022557.1|FK022557
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
EST: gi|51344418|gb|CO985151.1|CO985151
EST:     CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCG                         AAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG
genomic: CATTCTATGGACTCTTTAATCTCTTCTCTGGTTTCTTTATCCCAAGACCGgtgagtacca ... ggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCATC
                                               cttttc  CT-rich tract
      ttacataatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaccattctaatttcgttattatattgaaacaaacatatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA