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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgttattatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA

Basic information

species Glycine max
transcript GLYMA02G17430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgttattatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA
|| ||  ||   ||    ||||     |   | |  |  || || || ||   || |  |        || |  ||||| |||       ||||  |||     |||| ||||| || || || || ||||| || |||||||||||||| || || || || |||||||||||||| ||||| || || ||||| ||||| || 
gtaagagaagatccgc-cgcttcgcgctgtgcgtggtggttgtttggtttggtttctgatcggctagggtttgaaacttttgt----gtggtttttttt----tagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG

upper sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038606_T03 (Zea mays), 3'ss of exon 2
----gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgtt------attatatgtgtagaac-ttgtgttaatactgtt-tgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA-
    |   || |   ||| |  || || || || |    |  |||||   |  |   |    |||      ||| |  ||   || | |||  || | ||| || |||| |    ||||| ||||| ||||| ||||| ||||| || ||||||||  |||| ||||| || || |||||||||||||||||  | || || ||||| ||||| ||  
gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattgttagtcctgaccgttgaattgaaactattgtgatct----cagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAGG

upper sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 2
----gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgtt------attatatgtgtagaac-ttgtgttaatactgtt-tgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA
    |   || |   ||| |  || || || || |    |  |||||   |  |   |    |||      ||| |  ||   || | |||  || | ||| || |||| |    ||||| ||||| ||||| ||||| ||||| || ||||||||  |||| ||||| || || |||||||||||||||||  | || || ||||| ||||| || 
gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattgttagtcctgaccgttgaattgaaactattgtgatct----cagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAG

upper sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G095114_T01 (Zea mays), 3'ss of exon 2
gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattg-------ttattatatgtgtagaa-cttg--tgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA
       ||   ||| |||  |   || |  | || |  ||||| | ||    |||||         |||| | | |   ||  | ||   ||||| ||| ||||  || |  ||||| ||||| ||||| ||||| ||||| || ||||||||  |||| ||||| || || |||||||||||||| ||  | || || ||||| ||||| || 
-----gtaagatcccggtgtctggcttctttcgtcgtcgtttttggcgtgtgattattcgttcagtctattgtttatcctgagtcctgaccgttaaaactttttgtgttct--cagCTCGTGGAGCTGAAGAATGGTGAGACGTACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCACCTTAGGGAGGTTATTTGCACCTCAAAG

upper sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtcaaacc----ccctgtgctttatttttaccctctttttttttagggttacctta--ttgttattatat-----gtgta---gaacttgtgtt------aatactg---tttgatttgt---aacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA
|||||| |||      ||||    |  | ||||    | | |    | | | | |  |||  |    |||  ||      | ||   ||||||   ||      |||  ||    ||| |||||      |||| ||||| || || ||||| ||||| || || ||||| ||||| ||||||||||| ||||||||||||||||| || |||||||| ||||| || || 
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG

upper sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgttattatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA
   |   | | |    ||   |||||||   | ||||||  | | | |  |     | | |||| || || || |  ||        | ||||    ||||  ||| ||||||| |||||||||||||| ||||| || || || || || ||||||||||||||||||||||||||||| || |||||||| || || || |||
---acatatagcataggtctattattttcctcttcttttcctctggtgagatggc-taggtatttta-gtatatattttacaa-gtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA

upper sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
---gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgttattatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA
     ||   ||||   | | || |   | | |     |||| ||| || |||| | | |   |     |  |||  ||||| |  |  |  ||| ||  |||| | || ||||||| || |||||||| || ||||| || ||||| |||||||| |||||||| ||||||||||| ||||| || ||||| || |||||||| |||
cctcagatgaaaacaagcagagcctcgatgtaaa---attttctttaagagttagcatctcacttcgtgacctgt--aacttatactgct--tgtatg--ttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA

upper sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S36_327V6.2 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------gtgagtcaa--accccctgtgctttatttttaccctctttttttttagggttaccttattgttat-tatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA
                                                                          | |  | |  |     |||||   | | | | | | || | |  |     |     || ||||  |  || | |      |    | |    ||  |   | |  ||||| || || || |||||||| |||||||||||||| || || || || |||||||||||||||||||| || || || ||||| ||||| ||||| || 
gtacgggtcacctttgccataacacttcttgaatatattctttggaacatcatgagaaaagatagaatttcacataatgcgaggagttgttgtgcacgactgtaatcattttatatcctgca--tgttggatcgttacatggatcttttaggtctaacatgacctcgtcggtaatctg-cagCTTGTCGAGCTCAAAAATGGAGAGACTTATAACGGCCATTTAGTAAACTGTGATACATGGATGAACATTCACCTACGTGAAGTTATTTGCACCTCAAAG

upper sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10085 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgttattatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA-
                                                     | | || | || |  || |    |||    | | |   || | || |    |||| ||||| || || ||||| |||||||| || ||||| ||||| |  || ||||  ||||||||||||||||| |||||||| ||||| || || ||  
----------------------------------------------------gtgagtgatgttcttcgtttccttctttgtctgaaa--attcgcttgg--gtagCTAGTGGAGCTCAAGAATGGAGAGACTTACAATGGGCATTTGGTGAGCTGCGATAGCTGGATGAACATCCATCTACGAGAAGTTATTTGCACTTCCAAGG

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|7639290|gb|AW733616.1|AW733616
EST:     CTTCCCCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCCATG                         CTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGT
genomic: CTTCCCCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCCATGgtgagtcaaa ... tttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGT
EST: gi|193406386|gb|FK373035.1|FK373035
EST:     CTTCCCCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCCATG                         CTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGT
genomic: CTTCCCCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCCATGgtgagtcaaa ... tttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGT
EST: gi|254324586|gb|GR834011.1|GR834011
EST:     CTTCCCCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCCATG                         CTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGT
genomic: CTTCCCCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCCATGgtgagtcaaa ... tttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGT
EST: gi|193581035|gb|FK535976.1|FK535976
EST:     CTTCCCCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCCATG                         CTGGTGGAACTGAAAAATGGGGAGACTTATAA
genomic: CTTCCCCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCCATGgtgagtcaaa ... tttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAA
EST: gi|298174084|gb|HO017420.1|HO017420
EST:     CTTCCCCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCCATG                         CTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGT
genomic: CTTCCCCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCCATGgtgagtcaaa ... tttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttattgttattatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA
     ttgttattatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgttattatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT