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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttttcagtaacaaaactccagaccaacttgtaatttgttttatatattttacctgatgttggaatgttcgtgaaatctgtttttgttccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGTCTGAACTATTATGCATAGGCTGGATTGTGGAACAAGCTAT

Basic information

species Glycine max
transcript GLYMA10G29250.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
ttcttttcagtaacaaaactccagaccaacttgtaatttgttttatatatttta-cctgatgttg-gaatgttcgtgaaatctgtttttgttccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGTCTGAACTATTATGCATAGGCTGGATTGTG-GAACAAGCTAT
                        |   |  | |  || || |||    || || | | | | || | ||| |  || |     |  |   |      | |||||||||| |||||||| ||||||||||| |||||||| ||||| ||||||||||||||  |||| || || || || |     || |  | |||  ||  
----------------------gtatgcatatatctttcgtcttagtggttgtaactttaggatgtggatgat-atggaggaaatggtaaatgtgtgtgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTTTATGTACACTCTT-

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
ttcttttcagtaacaaaactccagaccaacttgtaatttgtt-ttatatattttacctgatgttggaatgttcgtgaaatctgtttttgt-tccaaacgt--agGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGTCTGAACTATTATGCATAGGCTGGATTGTGGAACAAGCTAT-
    |   |   ||| |||||   |   | |||   ||| |  || | || |||      | ||  || | | | |   |||||| |||| |      ||  |||||||||| || || || ||||||||||| || |||||||| || ||||||||||||||  ||||||| || || |   ||    | |   |  |  ||| 
---gtaaaaaagacagaactcttaat-gatttgagctttatgattgtgtagtttggtctgttttttaa-ggtggggttctctgttgttgtgtttgtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCT-CTCTCTCATCATTTATT

upper sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
ttcttttcagtaacaaaactccagaccaacttgtaatttgttttatatattttacctgatgttggaatgttcgt-gaaatctgtttttgttccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGTCTGAACTATTATGCATAGGCTGGATTGTGGAACAAGCTAT
     ||| || |      |    || | |  ||| |     || |    | ||||    |    | |  |  | | | | |    ||| |   |    |||||||||| ||||| || || |||||||| |||||||| || || ||||||||| ||||  | || |||||||||||||||         |||| |  ||
-agagttctgtgatgtttttatgtactatcacgtattgaaacttttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGCTTCTCCTCCAAACATGTCAT

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|23732877|gb|BU764614.1|BU764614
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAG                         GTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
EST: gi|4397504|gb|AI496501.1|AI496501
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAG                         GTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
EST: gi|6847857|gb|AW350147.1|AW350147
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAG                         GTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
EST: gi|58017156|gb|CX703898.1|CX703898
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCTTTACGCCGTGATGCAACTGAG                         GTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
EST: gi|7591094|gb|AW706834.1|AW706834
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAGCTGAG                         GTGAACCACGAGGATTGTAATGAAGGTATTATGCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
EST: gi|6095148|gb|AW119815.1|AW119815
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAG                         GTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
EST: gi|6482334|gb|AW201601.1|AW201601
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAG                         GTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttc ... ccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattttacctgatgttggaatgttcgtgaaatctgtttttgttccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGTCTGAACTATTATGCATAGGCTGGATTGTGGAACAAGCTAT
        acctgat  putative branch site (score: 4)
                                 tctgtttttgttcc  putative PPT
                                     tttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttttcagtaacaaaactccagaccaacttgtaatttgttttatatattttacctgatgttggaatgttcgtgaaatctgtttttgttccaaacgtagGTGAACCACGAGGATTTTAATGAAGGTATTATTCAAGTCCAAGCAAAGAAGAAAGCAAGTCTGAACTATTATGCATAGGCTGGATTGTGGAACAAGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - -aacaaaa
- - - - - - - - - - ccagacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgttg