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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatagtcatactaatttccttttgtaattctttatatatcctcatattcatctatgcttcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC

Basic information

species Glycine max
transcript GLYMA06G01520.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 5
gtaatagtcatactaatttccttttgtaattctttatatatcctcat---attcatctatgcttcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC
    ||  | |    | |||  |  | ||      |||  || |      | |||   |   | |||  |   | ||| | ||||| ||||| || |||||||||||||| ||||| |||||||||||||||||||||   || ||||| ||||||||||  || | | | || || |
---gtacacttctatagttctatacgaaaaaaaacataattcttttcggaagtcaaaaactgtacttattatatgcagGCAAATCCAGAAATCGTGAAAAGATGGAGCAACGAAGTGCAGGAAGCTGTTCAATCAAGATTTGCACTTGTGCAATTTCATGGCCTAGCTCTTCTTCACC

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 5
------------------gtaatagtcatact--aatttccttttgtaattctttatatatcctcata-----ttcatctatgct-tcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC
                  ||  | | | |  |  |||| | | ||  |         | ||||| | |     ||  | | |    | ||  |     ||||| | ||| ||| |||| ||||| |||||||||||||||||||| ||||| || || ||||| || ||||| ||||||||||| || | | | || || |
gtatgtgcaaaacgtttagtctttgcctttatgcaattgcatattacagccagacccaaatccttacaaatgttttgtttgtatggttttattctgagcagACAAGTCCAGAAGTTGTGAAAAGGTGGAGCAATGAAGTTCAGGAGGCTGTACAGTCGAGAGCTGCTCTTGTTCAATTTCATGCCCTTGCTCTTCTTCACC

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 5
----------------------------gtaatagtcatactaatttccttttgtaattctttatatatcctcat-at-tcatctatgcttcttgcttatta-cagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC
                                | |  ||| |  |     || ||    || || ||||  | || || |  || |    | |   |||||  ||||||| ||| ||| |||||||||||||||||||||||||||| || ||||| || |||||||| || ||||| ||||||||||| || | | | || || |
gtatgtcctgcagttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACC

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 4
-----------gtaatagtcatac-taatttccttttgtaattctttatatatcctcatattcatctatgcttcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC
            |  ||  ||||  ||     || ||||      ||   || |   || ||     |   |   | |    ||||| | || || |||||||| |||||||||||||| ||||||||||||||||| |||||||||||  | ||||| || |||||||  || | | | || || |
gtactagcataattctatgcatatataccgatctcttgtttaaggttggttaactgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 5
---------------------gtaatagtcatactaatttccttttgtaattctttatatatcctcatattcatctatgcttcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC
                     |  ||| |  ||||| |||      |   ||  || | | |  | || ||   |     ||  | ||  |  ||||| | ||| ||| |||||||||||||||||||||||||||| || ||||| || |||||||| || ||||| || |||||||| || | | | || || |
gtatgtcctgtgctccacttggatatattgttactagtttgtggcagct-ttagttcttttttattatgttttccacatgtttgtactattggcagACAAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAGTTTCATGCCCTTGCTCTCCTTCACC

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaatagt--catactaatttccttttgtaattcttta--tatatcctcatattcatctatgcttcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC
|||    |  || || ||     ||  |||  |  |||  | ||   | ||  | || |  |  | |||||  || ||||| || || |||||||| ||||||||||||||||||||||| |||| | ||||||| ||| |||||||||| || || ||||| || | |||||| ||||
gtaccttttacacaccaaaactattaggtagcttcttaattgtaatgttatgcttatattcgtatattgctgttttcagACAAACCCAGAAATTGTTAAAAGATGGAGCAATGAAGTTCAAGAAGGTATTCAATCCAGATCAGCCCTTGTTCAGTTCCATGCCCTAGCTTTGCTCCATC

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 5
---------------------gtaatagtcatactaatttccttttgtaatt--ctttatatatcctcatattcatctatgcttcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC
                      |  |  | || ||| ||   | ||  ||||  | |  || || |||  ||      ||  || ||  ||   | |||| || || || || || | ||| ||||| |||||||| |||||||||||||||||||| ||||| ||||| ||||||||||| || | | | || ||||
gtacaattgggttgtgtgtagattttttttattctatttatatatttaaattatcctcttacatgctctaataatatgattattatttttttggatagACAAACCCAGAGATAGTGAGAAGGTGGAGTAATGAAGTACAGGAAGCTGTTCAATCAAGGGCAGCACTTGTGCAATTTCATGCCCTAGCTCTCCTGCATC

upper sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------gtaatagtcatactaatttccttttgtaattctttatatatc-------ctcatattcatctatgcttcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC
                    |||  || ||   ||   |   |  | | | ||   ||| |       ||  |  |||| |    |   |  || ||  |||  || || |||||||| ||  | |||||||||||||||||||||||||| || || | |||| | || || || || || |   |||  ||||| ||||
cgaatgtttttctgttcttttaaacgttatttaaacaacaaatgatgaattttctgataacagcttctcttttgctcattttaaatctgtaatt-ttgtagAGCAACCCCGAAATTGTGAAGCGCTGGAGCAATGAAGTTCAGGAAGCTGTCCAGTCTAAAGCACCTCTCGTTCAGTTCCACGGTTTGGCATTGCTTCATC

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|193605010|gb|FK556324.1|FK556324
EST:     ATCCAGTTGTTGCAAGTGCTGCTCTAGTTAGTGGCATTCATCTACTCCAG                         ACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTT
genomic: ATCCAGTTGTTGCAAGTGCTGCTCTAGTTAGTGGCATTCATCTACTCCAGgtaatagtca ... cttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgtaattctttatatatcctcatattcatctatgcttcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC
                                      cttcttgctt  CT-rich tract
      taattctttatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatagtcatactaatttccttttgtaattctttatatatcctcatattcatctatgcttcttgcttattacagACGAATCCTGAAATTGTAAAAAGATGGAGCAATGAAGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTACATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG