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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgattacacttcttgaactttacaatcatcttaagcacatccaccaccattttgaatgacatgatttccttacgacatacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG

Basic information

species Glycine max
transcript GLYMA07G31090.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
gtttgattacacttcttgaactttacaatcatcttaagcacatccaccaccattttgaatgacatgatttccttacgacatacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG
              ||   | |||    |  |   ||  | ||   || |     ||  || | | |||| ||   |  | |  || | ||     ||    | ||||  || ||||||||||||||||| |||||||| ||||| |||||||||||||||||||| || || ||  | || || |||||  | ||  | ||||  | |      |
------------ccctaagattttgttcttgttgcaataaaattt-ccgctgcaatgc-tgtcttcattttctcctgggagatgtc-attctgaacttggccg-tttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG

upper sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 11
gtttgattacacttcttgaactttacaatcat-cttaagcacatccaccaccattttgaatgacatgatttccttacgacatacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG
          |  |     |    |    ||| ||||   ||||   | | | |||   | | ||   |||| ||       |   | | | | || |   |         || |||||||||||||||||||||||||| ||||| || || || ||||||||||| || || ||  | || ||  ||||  | ||| | ||||| | ||  | | 
----------aggttcaacatagcatggacattcttacatacattt-caatcgtttctta-gtcaaattttcattttagatcatgaccattgattgctcactcaac-----atgcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCCGCAGAGATGAAACGTGAGGCGGCACGTGGTGCTCTGAGCTCCGCATTCTGATGAAACATGCCTT

upper sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------------------------------------gtttgattacacttct-tgaactttacaatcatcttaagcacatccaccaccattttgaatgacatgatttccttacgacatacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG-
                                                                                      | |    | |  | | |  |   |   || || | || |  |   |  |   ||||  |||| || | |||   |  |     || |     | ||||      ||    || |||||||| |||||||||||||| || ||||| || |||||||||||||| || || ||  | ||||| || ||| |||| ||  | | ||  ||||   | | 
gtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgttttt--atgaaataaattctcaagta---gtctatctgagccgttttgacatttgtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCTATGCGGGCAGCTTTTTAAT-TATCAGAAAAGA

upper sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
gtttgattacacttcttgaactttacaatcatcttaagcacatccacca--ccattttgaatgacatgatttccttacgacatacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG
                            |||  ||      ||| |||   | | |||   |||    | |||  |  ||||||| |   | |      | |||||   ||  | |||||||| ||||||||||||||||| ||||| |||||||| |||||||| || || ||  | ||||| |||||||| || ||| | | |        |  | 
---------------------------gtcagttttctattatcaaccgttctaattttcctgaaccaacttcagtgtgacatacttgagccc------tttttggaccgc-gtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA

upper sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
--------------------------------------------gtttgattacacttcttg--aactttacaatcatcttaagcacatc-caccaccattttgaatgacatgatttccttacgaca--tacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG
                                            || |    | | |  ||   ||| |     |  | |      ||||  |    |  ||| | |  ||    |||   | || |  |   |  |   | | ||  | ||   |  | | |||||||||||||||||||||||||| ||||| || ||||| |||||||| || || || ||| | || || ||||||  |||  | ||||  | | | |  |
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagtttcaattattctagaagagagctgttttgagatattattgttctgaacttgttt-cagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG

upper sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 11
--------------------------------------------gtttgattacacttcttgaactttacaatcat----cttaagca---catccaccaccatt-ttgaatgacatgatttccttacgacat--acctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG
                                            ||||||  | |       || |     |||||    |  | | |   |||    ||  ||| ||  ||    ||| ||| ||| |   |  ||  ||   || |   |  |   |   || | ||||||||||||||||| |||||||| ||||| || ||||| ||||| ||||| || || ||  |  | ||  | ||  | ||  | ||||| |    |  | 
gttggttgaatctgttctttgttcaataaatcctccatcatacagtttgagaaaaaaaaagcaa-tccgtcatcatagaacccagggatctcattgtgcattattcttccatttattgagttctttatgttcttcacacctgaccattaagttctctctcaact-tgcagCAAGTATACATGTATTTCCGTGGAAGTGGAAAAGCTGCAGAGATTAAACGTGAGGCAGCACGTAGTGCTCTAAGTTCAGCCTTCTGATGAACATCTTTTT

upper sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 11
--------------------------------------------gtttg----attacacttcttgaactttacaatcatcttaag--cacatccaccaccattttg--aatgacatgatttccttacgacat--acctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG
                                            |||||    |  | |  || |  |   ||| |  | |    |  |  ||    ||   || |   |||    | |  |  ||| |   |  ||  ||  ||| |   |  |   |   || | |||||||| |||||||| |||||||| ||||| || ||||| ||||||||||| || || ||  |  | ||  | ||  | ||  | ||||| |   |    |
gttggttgaatctattctttcttcaatggatccttcatcatactgtttgagagaaaaaaaatccttcatcatactacaacccagggatcttattgtacattgttctctcaatttagtaaagtttttatgttcttcacgcctgatcattaagttctctctcaact-tgcagCAAGTCTACATGTATTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAACGTGAGGCAGCACGTAGTGCTCTAAGTTCAGCCTTCTGATGAACATAGGGCG

upper sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
gtttgattacacttcttgaacttta-caatcatcttaagcacatccaccaccattttgaatgacatgatttccttacgacatacctctactcactgt-ttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG
||   | | | |||    |    ||  |||||    ||||| | | ||| |   |   |||   |||| |  | | |  |     |  |||   | | || |||    || | | ||||||||||| ||||||||||| |||||||| || || ||||||||||| || |||||||| || ||||| |||||||||||| | | | ||  ||||    
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgct---aataggatgaat--catgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC

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|254315267|gb|GR830260.1|GR830260
EST:     GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAG                         CAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
genomic: GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAGgtttgattac ... tgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
EST: gi|10255230|gb|BE822996.1|BE822996
EST:     GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAG                         CAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
genomic: GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAGgtttgattac ... tgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
EST: gi|193400696|gb|FK368337.1|FK368337
EST:     GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAG                         CAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
genomic: GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAGgtttgattac ... tgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
EST: gi|23728768|gb|BU762445.1|BU762445
EST:     GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAG                         CAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
genomic: GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAGgtttgattac ... tgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
EST: gi|208043660|gb|GD843150.1|GD843150
EST:     GGGTCATTCAG                         CAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
genomic: GGGTCATTCAGgtttgattac ... tgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
EST: gi|10255778|gb|BE823488.1|BE823488
EST:     GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAG                         CAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
genomic: GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAGgtttgattac ... tgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
EST: gi|6964344|gb|AW433037.1|AW433037
EST:     GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATATGGGTCATTCAG                         CAAGTATACATGTACTTACGTTGCAGTGGTAACGCTGCTGACATGA
genomic: GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAGgtttgattac ... tgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGA
EST: gi|14991928|gb|BI317601.1|BI317601
EST:     GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAG                         CAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG
genomic: GATTTGGATTATTCTGCATTGAAACGTTGATCAGCATTTGGGTCATTCAGgtttgattac ... tgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgatttccttacgacatacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG
                         tactcac  putative branch site (score: 1)
                                  tttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgattacacttcttgaactttacaatcatcttaagcacatccaccaccattttgaatgacatgatttccttacgacatacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA