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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agattatattaaaaaaattgtatagttttttcctagatacctttaatgttctccatgttatgatgtttttgttcatatttaatgcaattatgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG

Basic information

species Glycine max
transcript GLYMA10G04480.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 9
agattat--attaaaa---aaattgtatagttttttcctagatacctttaatgttctccatgttatgatgtttttgttcatatttaatgcaattatgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG
|   | |   ||  ||   |   |  || ||| |||  |   | | | | ||| |  ||| ||| || |   ||| |  |  ||| ||  || | ||||  ||||||||| || |||||||| || |||||| | ||||| | ||||||||| ||| | || ||||||||||||||||| ||||| |||||||| ||||||||||
aatctgtttgttggaatccatgctaaattgttattttgtttttgcatgttatgcttccca-gtt-tggt-catttataaactttttatataact-tgtat-tcagGTTGTGGAAGCATTTAAGATTTTGACTTCCGATGATAGAGTGAAGGCTATTCTAGTGAACATTTTTGGTGGTATCATGAAATGTGATGTGATAGCAAGTG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 9
------------------------------------------------agattatattaaaaaaattgtatagttttttcctagatacctttaatgttctccatgttatgatgtttttg----ttcatatttaatgcaatt---atgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG
                                                     || |||||    |       ||||  | | |   |  ||||| | |  || |     |||  ||||    | | ||| |  |  ||||   ||   |  |||||||| || || ||||| ||| ||||| | ||||| | ||||||||||||| | || |||||||||||||| || ||||| |||||||| ||||||||||
gtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccc-tgacgccattttgacattgtagc--ttaatttgccgcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccagGTTGTGGAAGCTTTTAAGATACTGACTTCAGATGATAGAGTGAAGGCAATTCTAGTGAACATTTTTGGTGGCATTATGAAATGTGATGTGATAGCAAGTG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 9
---agattatattaaaaaaattgtatagttttttcctagatacctt-taatgttctccatgttatgatgtttttgttcatatttaatgcaattatgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG
    | |  |  |   | | |  |  | ||   | | |   |  ||    |||| |  ||      || | ||| || ||  ||||    ||||||| || ||||| || || ||||| |||||||||||||||||||| || || || |||||||| || ||||||||||| || |||||||| |||||  | ||||||||||
tcttgctctttctctcacattgatgcacttaaatacaactcaagttactgtgttataaataaagatatatatttattaattcttaa----attatgtgaaacagGTGGTGGAAGCATTCAAAATATTGACTGCTGATGATAAGGTCAAAGCAATTTTAGTGAACATTTTTGGAGGAATAATGAAATGTGACATAATAGCAAGTG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 9
agattatattaaaaaaattgtatagttttttcctagatacctttaatgttctccatgtta-tgatgtttttgttcatatttaatgcaattatgtaaatc--------agGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG
           |   |||    ||   |     ||| |     |  |||    ||  |   || | | || ||| ||| ||||   |  |   ||  ||        ||||||| || || ||||||||  ||||| | ||    | |||||| || ||| |||| |||||||||||||| || ||||||||||||||||| ||   ||
---------ccatgtaatcaactaccatagctgtagttgttgctgttgtgaagcaattgggtggtatgttcgttgatagttaaccgaccttgatatgtcgcttgtgcagGTTGTGGAAGCTTTTAAAATTCTGACTTCCGACACGAGAGTGAAAGCTATTCTGGTGAACATTTTTGGTGGGATCATGAAGTGTGATGTTATTGCTGCTG

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|193672162|gb|FK617566.1|FK617566
EST:     GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAG                         GTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
genomic: GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
EST: gi|192311647|gb|FK004866.1|FK004866
EST:     GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAG                         GTTGTTGAGGCATTT-AAATATTGACTGCTGATGACAAAGTGAAGGCAATT
genomic: GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
EST: gi|192308760|gb|FG999785.1|FG999785
EST:     CAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAG                         GTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
genomic: CAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
EST: gi|254325002|gb|GR834427.1|GR834427
EST:     GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAG                         GTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
genomic: GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
EST: gi|298179372|gb|HO027843.1|HO027843
EST:     GTACTCCTGTCAATTTTCTGGATGTAGGTGGCGATGCCTCTGAAAACCAG                         GTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
genomic: GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
EST: gi|7326644|gb|AW620442.1|AW620442
EST:     GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAG                         GTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
genomic: GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
EST: gi|51336677|gb|CO980543.1|CO980543
EST:     GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAG                         GTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
genomic: GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
EST: gi|151406201|gb|EV276016.1|EV276016
EST:     GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAG                         GTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
genomic: GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
EST: gi|6727069|gb|AW311423.1|AW311423
EST:     GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAG                         GTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
genomic: GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
EST: gi|12689320|gb|BG155656.1|BG155656
EST:     GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAG                         GTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
genomic: GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT
EST: gi|22523849|gb|BU082660.1|BU082660
EST:     GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAC                         GTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGCGAAGGCAATT
genomic: GTACTCCTGCCAATTTTCTGGATGTAGGTGGCAATGCCTCTGAAAACCAGgtaatgtttt ... tgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttctccatgttatgatgtttttgttcatatttaatgcaattatgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG
                               atttaat  putative branch site (score: 4)
                             atatttaatgcaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agattatattaaaaaaattgtatagttttttcctagatacctttaatgttctccatgttatgatgtttttgttcatatttaatgcaattatgtaaatcagGTTGTTGAGGCATTTAAAATATTGACTGCTGATGACAAAGTGAAGGCAATTTTGGTTAACATTTTTGGTGGTATAATGAAGTGTGATGTTATAGCAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcaa