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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAGGCATCAGCGGGCACATTCTCTGTGGTGGCAAGCTTCTGAGCAGGGTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtggtttgacgatgcgcaatgctgtgaattcaatttattggccattgtgctctcttttgcctactacaccttttcactttctcgtgtttttcccccccttctgtcag

Basic information

species Glycine max
transcript GLYMA05G33770.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G33770.2 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os03g15350.1 (Oryza sativa), 5'ss of exon 4
AGAAAGGCATCAGCGGGCACATTCTCTGTGGTGGCAAGCTTCTGAGCAGGGTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtggtttgacgatgcgcaatgctgtgaattcaatttattggccattgtgctctcttttgcctactacaccttttcactttctcgtgtttttcccccccttctgtcag
 ||||| ||||  || |||||| |||||||||||||||| || ||||||||||| ||||||||||| ||  | ||||| || || || |||||||| |||||||||| |   || || |    |  ||   ||   |  |  ||   | ||  ||    ||||      |   |     |||||  |    |     |  |    ||    
GGAAAGACATCTCCGTGCACATGCTCTGTGGTGGCAAGCATCCGAGCAGGGTAACGAACATGCTGCCTTGTTAATTGGTGACGCCTACTACTATGGCCGGgtatgtgtt---acaatccatgttcttggttatgagaaattctga--aatgctcttgaatttgttag--aggacagaggacttttcctaaataccttcatcaaattg----

upper sequence: GLYMA05G33770.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G372398_T03 (Zea mays), 5'ss of exon 2
AGAAAGGCATCAGCGGGCACATTCTCTGTGGTGGCAAGCTTCTGAGCAGGGTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtggtttgacgatgcgcaatgctgtgaattcaatttattggccattgtgctctcttttgcctactacaccttttcactttctcgtgtttttcccccccttctgtcag
 ||||| ||||  || || ||| || ||||||||||||| || |||||||||||||| |||||||| ||  | ||||| ||||| || |||||||||||||||||   |      ||  | |||  |   ||| ||    |||||   ||  |  | ||| |||    |     | |  |    ||| | |    |  |   ||       
GGAAAGACATCTTCGTGCGCATGCTTTGTGGTGGCAAGCATCCGAGCAGGGTAATGAGCATGCTGCATTGTTGATTGGCGATGCCTACTACTATGGTCGGgtatgcactacagtcatctg-aatttttaaaatacataaaattgg---ttagggccgcttgtgctagttttgaatctgtatacactcctttcggactacatttt-------

upper sequence: GLYMA05G33770.2 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G146386_T01 (Zea mays), 5'ss of exon 2
AGAAAGGCATCAGCGGGCACATTCTCTGTGGTGGCAAGCTTCTGAGCAGGGTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtggtttgacgatgcgcaatgctgtgaattcaatttattggccattg-tgctctcttttgcctactacacct-tttcactttctcgtgtttttcccccccttctgtcag
 ||||| ||||  || |||||| || |||||||||| || || |||||||||||||| |||||||||||  | ||||| ||||| || |||||||| ||||||||   |      ||  |  |   |   |||  |     ||||  |  | ||||     | |  |  |  | || | |||||   |   | | |  |              
GGAAAGACATCTTCGTGCACATGCTTTGTGGTGGCATGCATCCGAGCAGGGTAATGAGCATGCTGCTTTGTTGATTGGCGATGCCTACTACTATGGCCGGgtatgcactacagtcatctg--acttttaaaatatataaagttggttagggctgcttgtgctagaattttgaatctgtatcactccttttggctgtagcttt-----------

upper sequence: GLYMA05G33770.2 (Glycine max), 5'ss of exon 2
lower sequence: AT1G73570.1 (Arabidopsis thaliana), 5'ss of exon 5
AGAAAGGCATCAGCGGGCACATTCTCTGTGGTGGCAAGCTTCTGAGCAGGGTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtg-------gtttgacgatgcgcaatgctgtgaattcaatttattggcc--attgtgctctcttttgcctactacaccttttcactttctc-gtgtttttcccccccttctgtcag----------------------------------------------
 || |||||  | ||||| |||||| |||||||||  || ||||| ||||| || ||||||||||| || || ||||||||||| |||||||| ||||||||| ||        | |||| | |    |||  ||   || |     || |     |||||    | | |   |   | ||| |||    ||||   | |    |    | | |   | |                                               
GGAGAGGCACGATCGGGCTCATTCTTTGTGGTGGCGTGCCTCTGAACAGGGAAACGAACATGCTGCATTGCTTATTGGAGATGCATATTACTACGGTCGGgtaagtctacttacgcttgaagtttatgaattgtgaacatacggacaatggatataattgtcacttatctcatcccattcacatttgatttttccaagagaacatatttctcattcatgaaatctagacgttaactgattctatgaggctcatactcatgttcacag

upper sequence: GLYMA05G33770.2 (Glycine max), 5'ss of exon 2
lower sequence: AT1G18260.1 (Arabidopsis thaliana), 5'ss of exon 4
AGAAAGGCATCAGCGGGCACATTCTCTGTGGTGGCAAGCTTCTGAGCAGGGTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgt--ggtttg-acgatgcgcaatgctgtgaattcaatt-tattg------gccattgtgctctcttttgcctactacaccttttcactttctcgtgtttttcccccccttctgtcag------------------
||| || ||| |||||||||||||| |||||||||  || ||||| || || ||||||||||||||| | || ||||||||||| ||||||||||| |||||  ||     | | |  |    | |   | ||||   |||    |||      |  |   || |    || ||     | | |||   ||||  |||  |  ||| | | ||||| ||                    
AGAGAGACATGAGCGGGCACATTCTTTGTGGTGGCGGGCCTCTGAACAAGGCAATGAACATGCTGCTCTGCTTATTGGAGATGCATATTACTATGGCCGGgtgagtttacctcgtataagaaactagattatgaacctaataacgttgagacatgtaacaatgattgaattagctagaaaaaacttgatacttg-tcgcctgattctctctcttctctcgttctttgatctctaaatag

upper sequence: GLYMA05G33770.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv17s0000g02280.t01 (Vitis vinifera), 5'ss of exon 4
AGAAAGGCATCAGCGGGCACATTCTCTGTGGTGGCAAGCTTCTGAGCAGGGTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtggtttgacgatgcgcaatgctgt--gaattcaat--------ttattggccattgtgctctcttttgcctactacaccttttcactttctcgtgtttttcccccccttctgtcag-------------------
|||||||| |||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| || || || ||||| ||||||||||||||||||||||  |  |    |   ||| ||||  ||  || |          |  ||    | ||   |  || ||    | | ||  | | | |||      |||||       |  |||                      
AGAAAGGCTTCAGCGGGCACATTCTTTGTGGTGGCAAGCTTCTGAGCAGGGTAATGAACATGCTGCTTTGCTGATCGGGGATGCTTATTACTATGGTCGGgtatgtgtctataaatgggttaatcctgtcggagctctaggtccaggacttctgattctagtatgcatttatgttctccatacaatgtaaattttcttaatttttatttatttattgtttaccttctttccctttctcag

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|58021435|gb|CX708176.1|CX708176
EST:     GTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGG                         GGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAA
genomic: GTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtggtt ... cttctgtcagGGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAA
EST: gi|58015158|gb|CX701900.1|CX701900
EST:     GTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGG                         GGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAA
genomic: GTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtggtt ... cttctgtcagGGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAA
EST: gi|192303882|gb|FG998234.1|FG998234
EST:     GTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGG                         GGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAA
genomic: GTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtggtt ... cttctgtcagGGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAA
EST: gi|6746941|gb|AW317397.1|AW317397
EST:     TAATGAACAT-CTCGCTTTACTCATTGNAGATGCGTATTACTATGGTCGG                         GGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAA
genomic: TAATGAACATGCT-GCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtggtt ... cttctgtcagGGTACTGCCAGGGATTATGAGCGAGCTGCTGAGGCTTATATGCATGCTAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAGGCATCAGCGGGCACATTCTCTGTGGTGGCAAGCTTCTGAGCAGGGTAATGAACATGCTGCTTTACTCATTGGAGATGCGTATTACTATGGTCGGgtatgtggtttgacgatgcgcaatgctgtgaattcaatttattggccattgtgctctcttttgcctactacaccttttcactttctcgtgtttttcccccccttctgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG