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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatcatagctgtcatttgtgtagttttgattgaattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG

Basic information

species Glycine max
transcript GLYMA02G03080.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
-tttatcatagctgtcat-ttgtgtagttttgattg--aattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
  | ||  |    |  |  ||  ||     | ||    |   | || | |   | ||||   ||||     | | || ||||| |  |      |  |||  |||||||||| |||||||| ||||||||||| |||||||||||||| ||||| || ||||| ||||| ||  | ||||||||| | ||  | ||||||
gctcatattgttcgatagattcagtgccgctaatcagtagaaaacacaatcc-tgctcttggagatgcatgtaacttttctatatcctct-cggtgttgt--agATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 3
--tttatcatagctgtca-tttgtgtagttttgattgaattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
   || |    |||  || |||||     ||       | |   ||  || | | |  || ||   |||| | |     | | |      |  || | |  || ||||||||||||| || ||||| |||||||| || |||||||| ||||| || ||||| ||||| ||  | ||||| || || ||||| ||||||
tggttgtgcctgctagcagtttgtagcaattcacccttaatgaaatgtttcagttttagtaag---tgatggttactaatgtttccccactctttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCCGGAAGCACTTACCGTACCAGGGATGAGATCTCAGGTGTAAGACAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G361693_T01 (Zea mays), 3'ss of exon 3
tttatcatagctgtcatttgtgtagttttgattgaattatcatagtttattctctgttagatttg---attgatttctcta-tcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
   |    |||  || |   || |  |  |       |  |||| ||  |||  |  |||   ||   | || || ||  |  | ||  | |   | | || || | ||||| ||||| || |||||||||||||| ||||||||||| ||||| || ||||| ||||| ||  | ||||| ||||| ||||| || |||
---aggcaagccttc-tccctgcaaatgcggagaggctcgcataattatttcatttctagtgctgaagaatggttactaaaaccctaaggttctatatatctagGTCCTTGAGATGGATACCTACAGATACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
------tttatcatagctgtcatttgtgtagttttgattgaattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
       |||   |||  |    |||       | | ||   | ||   ||  | |  |||  || |  || |      | |  |  ||||  || |    | ||||| ||||| |||||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||| | ||||| ||  ||||  | || |||
aggacccttaaactagacgaggcttg----acatcggttttgtgattccagactttcttct--taaagatgctgatcaccacggttctattcgttttatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G140150_T01 (Zea mays), 3'ss of exon 3
tttatcatagctg-tcatttgtgtagtt--ttgattgaattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
    | |||  || | | ||||  | ||  ||  |||  | || ||  |||| | ||   |       | || || ||  | | |  || |   | | || || | ||||| ||||| || ||||| |||||||| ||||||||||| ||||| || ||||| ||||| ||  | ||||| ||||| ||||| || |||
---gtgataagtgataacttgttcactttgtttgttggttcataattatttaatttcatgtgctgaataatggttactaaaccctcatgttctatgtatctagGTCCTTGAGATGGATACCTACAGGTACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G24180.1 (Arabidopsis thaliana), 3'ss of exon 3
tttatcatagctgtcattt-gtgtagtt-ttgattgaattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
 || | |   |  |||  | | || |   || || | ||| | ||| |  |||||||      |     |||      || | |    |||||| ||  ||||| ||||| |||||||||||||||||||| || |||||||||||||| || || ||||| ||||| || ||||||||||| ||||| |||||||||
-ttgtgaattcaatcacatagcgttgacatttatcgtatttttataatccattctctacctagtgattatgaccaacataccattgccattatt-tgcgcagATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
tttatcatagctgtcatttgtgtagttttgattgaattatcata-gtttattctctgttag-atttgattgattt---ctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
     ||||   ||  |   | | ||||  | |  ||| || |  ||||||||| |  ||  || ||  | |      |  ||    || | || |||| | ||||||||||| |||||||| ||||| ||||| || ||||| |||||||||||||| ||||||||||| || || ||||| || ||||||||||| |||
-----catataagtagtagctttggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
-tttatcatagctgtcatttgtgtagttttgattgaattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
 ||||   | | ||  | |  | |   | |  | | ||| ||||  |||  | |  | | || |  |||| ||| | | |||| |  ||  |  ||| ||||||||||||||||||||||| || |||||||| ||||| |||||||||||||| ||||| ||||| ||||||||||| ||||||||||||||||||
ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgact-aattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 3
tttatcatagctgtcatttgtgtagttttgattgaattatcatagt--ttattctctgttagatt---tgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
     |    |||  |||  |  | | ||   |  |  ||    ||  | ||| |   | |||||   | |||||||| ||| |||| |  ||  || ||| ||||||||||||||||||||||| || |||||||| ||||| |||||||||||||| || |||||||| || |||||||| ||||||||||||||||||
-----cccgcctgcaattctttcattctttgcttgagcatgtctgtcatcattttacatgagattgactaattgatttatctttcttctaaatgcttgtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGTACATACCGTACGCGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S201_84V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------tttatcatagctgtcatttgt-gtagttttgattgaattat--catagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
                                                               ||||    |  ||   | ||| | || |||   | | ||||  | ||    |    || ||    |||  |  ||| |||   ||||   || |    |  || || | || ||||| || |||||||| ||||| |||||||||||||| || |||||||| ||||| || |||||||| || ||||||||  |||||
gtaagtgatgctgttgttttcctaaccagcacatggatactttaccttcttctaatcatggggtttactccatttgctgtgtgttgcagctttacgtcagttatgtcgtaaccgagatgcttttg--cttgggttctttttctgaattatattttctggcatggagGTTTTGGAGATGGATACGTACAGATATCATGGTCACTCTATGTCTGACCCAGGCAGCACCTACCGAACCCGTGATGAGATCTCTGGTGTACGACAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S56_222V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------tttatcatagctgtca---tttgtgtagttttgattgaattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
                                         |  || ||     ||   |||    | |   |  | |  |  | |    ||  | || ||   ||||| ||||||||  |   | ||  || |    |  || || | || ||||||||||| || || ||||| |||||||||||||| || |||||||| || || || ||||| || || || |||||  |||||
gtaagttctgctggaaaatttgaaaatcattacgtcaatgctcgtcttattctccaggcttttctcaatggagtgttacgtgccgtcagctacgcact-ttgtttttgagtgatttctgaaaggtgtt--ttgtggaatgaagGTTTTGGAGATGGACACTTATAGGTATCATGGTCACTCTATGTCTGACCCAGGCAGCACCTATCGAACTCGTGACGAGATCTCCGGTGTCCGACAG

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|51338002|gb|CO981868.1|CO981868
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|254322999|gb|GR839912.1|GR839912
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|15664218|gb|BI701589.1|BI701589
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|58016185|gb|CX702927.1|CX702927
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTTTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|208280633|gb|GE080971.1|GE080971
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|15199292|gb|BI423757.1|BI423757
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|193721482|gb|FK662530.1|FK662530
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|58019317|gb|CX706059.1|CX706059
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|151406023|gb|EV275838.1|EV275838
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|19054086|gb|BM732753.1|BM732753
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
EST: gi|58016174|gb|CX702916.1|CX702916
EST:     AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT                         ATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT
genomic: AACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTTgtgagttgat ... ttctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG
                                    tattgat  putative branch site (score: 3)
                                             ttctgtcc  putative PPT
                               tatcttattgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatcatagctgtcatttgtgtagttttgattgaattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG

- - - - -gctgtca
- - - - - - - - tttgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttag