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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataatacaagttgctaggatttgcgtgtagtcacagagaaatggttttggtatcaaattcgtagaaccctaaaaaagaattctgaccttaatcata...

Basic information

species Glycine max
transcript GLYMA09G30410.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 5'ss of exon 2
TCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataatacaagttgctaggatttgcgtgtagtcacagagaaatggttttggtatca-aattcgtagaaccctaaaaaagaatt-ctgaccttaatcata--
||||||||| || |||||||| ||||||||| | ||||| |||||||| || || ||| | || || ||||| || ||||| || |||||||| |||||||||||  || |    | || | | ||| |  |  | ||   |  |||   |||  || |  ||| |||| |     ||   || ||  ||    | ||      
TCACTTCATGATCCCGTGGTTCGAGAGGCCGATCATCTACGATGTCCGAGCCCGCCCCAACCTCGTCGAGAGCACTTCTGGAAGCCGTGATCTCCAGATGgtaaa--attctg--tccttgcacttggggtttctgactaggtcatgtcgttgagatgatgatttgtagcatgtagaaggtgatttgttggttgtgatttgcga

upper sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os07g15880.1 (Oryza sativa), 5'ss of exon 2
TCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataatacaagttgctaggatttgcgtgtagtcacagagaaatggttttggt----atcaaattcgtagaaccctaaaaaagaattctgaccttaatcata
|||||| || ||||| ||||||||||||||  | || |||||||||||||| || ||| |||| || |||||||| ||||| ||  | ||||| |||||||||  |  | ||  ||  ||    |    | |  ||   |  |  ||  | |  |    ||| |||       |  ||  |   || ||     ||  ||    
TCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAAGCAGGGATCTCCAGATGgtacgtt-tgcatctttttaattctatattttcatcgttggaatgtgtgtatacttctcatctaatgatagatatacttgatttgatttgcatgctctatt---

upper sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 4
TCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataatacaagttg-------ctaggatt--tgcgtgtagtcacagagaaatggttttg--gtatcaaattcgtagaaccctaaaaaagaattctgaccttaatcata---
|||| | || ||||| ||||| || |||||  | |||||||| || ||||||   ||  ||||||||||||| ||||||||||| |||||||| |||||||||         | ||        |||  | |  || || || |||  |     ||||||||  || | || | | |   |  || |    |  |  |    |||| |||    
TCACCTTATGATTCCATGGTTCGAAAGGCCAATCATCTATGACGTTCGTGCAAAGCCTTATCTAGTTGAGAGCACATCTGGGAGCCGTGATCTCCAGATGgtattccgcttcatttcatcacttctaatactaatgggtataatca-ggtcgtgtggttttgtcgtgtgaactacatgataagcttatgttgtgtggta--tttaaacattcag

upper sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 3
TCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaat----------------aatacaagttgctaggatttgcg--tgtagtcacagagaaatggttttggtatcaaattcgtagaaccctaaaaaagaattctgaccttaatcata----
 ||| | || ||||| |||||||| |||||||| |||||||| || ||||| |||||  | || |||||||||||||| || || |||||||| |||||||||                   | |   |||   |  | |||| |  | |||| |  | ||| | |||   |  ||||  || ||    | |||       || ||   ||||   |     
ACACCTTATGATTCCTTGGTTTGAAAGGCCGGTCATCTATGACGTTCGTGCTCGACCTTACCTTGTTGAGAGTACATCCGGAAGCCGTGATCTTCAGATGgtactctgcttctactcctcccattttcagtcattttgttttgtgaatttagtgaatgtgaagtcgttc--gcttcaacatcataagctcttaagtttt--ttgtggttttaaaactttcag

upper sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 5'ss of exon 4
TCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataatacaagttgctaggatttgcgtgtagtcacagagaaatggttttggtatcaa--attcgtagaaccctaaaaaagaattctgaccttaatcata-----
|||| | || || || |||||||| ||||| ||||||||||||||||||||||| || ||||| || |||||||| || ||||| ||||| || ||||||||    ||||    || ||||   |||  | |||  | |  |   ||||| || |    |  ||  ||  |       ||  ||    |  |   ||   |      
TCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGAGCCGTGACCTCCAGATGgt----aatattgttttctagttcttgt-tatag--aaaatgttgtggttatgttgctgatcatgtgttcaggtgatgaagtgagacatagctgcaactttcagact

upper sequence: GLYMA09G30410.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 4
TCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataatacaagttgctaggatttgcgtgtagtcacagagaaatggttttggtatcaaattcgta---gaaccctaaaaaagaattctgaccttaatcata----
|||| | || || || |||||||| ||||| || ||||||||||||||| | || || ||||| || |||||||| || ||||| | ||| || |||||||||| |        || ||||   |||  |||||  | |  |   || || || | |  |    ||    |     | ||     |    |     |||   |    
TCACCTGATGATCCCATGGTTTGATAGGCCAGTCATCTATGATGTCCGTACGCGCCCTCATCTTGTGGAGAGTACTTCAGGGAGCCATGACCTCCAGATGgtaatt----ttgttttctagttcttgt-tgtag--aaaatgttgtgattatgttgttgatcatgtgtttgggtgatgaagtgagacatagttgcaaatttcagact

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|58019484|gb|CX706226.1|CX706226
EST:     TCTGGGAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCG-TGCCCCACCAAATTACN
genomic: TCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACC-AATTACC
EST: gi|207697115|gb|GD679966.1|GD679966
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
EST: gi|26059988|gb|CA802902.1|CA802902
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
EST: gi|33388681|gb|CA851888.1|CA851888
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
EST: gi|13562892|gb|BG551112.1|BG551112
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
EST: gi|13563054|gb|BG551274.1|BG551274
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
EST: gi|13563055|gb|BG551275.1|BG551275
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGTAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCTTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
EST: gi|151410209|gb|EV280024.1|EV280024
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
EST: gi|151411498|gb|EV281309.1|EV281309
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
EST: gi|192325059|gb|FK016170.1|FK016170
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
EST: gi|254318421|gb|GR832589.1|GR832589
EST:     CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATG                         GTGGAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
genomic: CACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
EST: gi|57574895|gb|CX547870.1|CX547870
EST:     TCTGGGAGTCGTGATCTACAGATG                         GTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT
genomic: TCTGGGAGTCGTGATCTACAGATGgtaaataata ... tgttatacagGTGAAAATTGGACTTCGAGTTCTTACTCGCCCGTTGCCCAACCAATTACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGAGTCGTGATCTACAGATGgtaaataatacaagttgctaggatttgcgtgtagtcacagagaaatggttttggtatcaaattcgtagaaccctaaaaaagaattctgaccttaatcata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaagaa