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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catacatgtgttgacttatgatagtcatctgcttggcacaaccttggattcattacttttactatttacctcttgaaaatgtttaaaactttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAATGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT

Basic information

species Glycine max
transcript GLYMA18G08370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G014313_T02 (Zea mays), 3'ss of exon 4
-catacatgt-gttgacttatgatagtcatctgcttggcacaaccttggattcattacttttactatttacct-cttgaaaatgtttaaaactttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAATGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT-
 || |||| |  ||  ||| || |  |  | |  |          |       ||    | || |     | | ||   | || |  |||  | |  |   |||| || || |||||||||||||| ||||| || |||  |||||| || ||||| || ||||| ||||| || ||||| |||||||| || || || || | 
ccacacatattatttgcttctgctgtttttgttatca-tgtgttatatatcctatcgtatgtagttgaagcatactcacatatatgcaaatatctttt---cagCAAAAATCCCCTTTCCATTGACTCAGAGATTCAGGGGAATGCTGCAAAATGGGATTGACCTGAGCACTGTTGATGTCAGCTATGTTAGTAGCCGGTCATG

upper sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------------------------------------------catacatgtgttgacttatgatagtcatctgcttggcacaacc--ttggattcat--tacttttactattt-acctcttgaaaatgtttaaaactttcatgc-------acaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAATGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT-
                                                                            |||  || | ||  | |      |||||||     | ||     |||  | |||  |||| | | | ||| |    |  | |   | |||  |||   ||         ||||||| ||||| |||||| |||| |||||||| || |||||| |||||||||| || ||| | ||||| || |||||||||||||| || ||||| || | 
gtttatttcctaaacaaagtgttttgcaattatttttcttggttacttcataaacagcaatcatgtatttgattttataactg-gctgtttcactgctttcatctgagaaac-cagttaattgtttccatgatactctaatttttttataattccatagcatctaaggcttctttgtttatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATGGCATTGACTTGAGCACTGTCGATGTTAGCTATGTGAGTAGTCGTTCCTG

upper sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0187g00220.t01 (Vitis vinifera), 3'ss of exon 4
-------catacatgtgttgacttatgatagtcatctgcttggcacaaccttggattcattacttttactatttacctcttgaaaatgtttaaaactttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAATGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT-
         | | | |  |   ||||   |    | |  ||   | |  |  |  |  || |   |||    |||     ||||  ||||    | |||  | | ||||||||||||| || || ||||| ||||||||| | || ||| |||| |||||||| ||  | ||||| ||||||||||||||||||||||||||||| | 
cttcacttttccgtataattgtttatatcaacattatttttttgataggcaagtttatatcaacatta----ttagaatctgaatctgtt----atttttttccccagCCAAGATACCTTTCCCCTTGACTCAGAGGTTTCGCTCCATGTTACAAAATGGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG

upper sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 4
-------catacatgtgttgacttatgatagtcatctgcttggcacaaccttggattcattacttttactatttacctcttgaaaatgtttaaaactttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAATGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT-
         | | | |  |   ||||   |    | |  ||   | |  |  |  |  || |   |||    |||     ||||  ||||    | |||  | | ||||||||||||| || || ||||| ||||||||| | || ||| |||| |||||||| ||  | ||||| ||||||||||||||||||||||||||||| | 
cttcacttttccgtataattgtttatatcaacattattttttagataggcaagtttatatcaacatta----ttagaatctgaatctgtt----atttttttccccagCCAAGATACCTTTCCCCTTGACTCAGAGGTTTCGCTCCATGTTACAAAATGGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG

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|193422023|gb|FK386696.1|FK386696
EST:     GACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCA                         GCCAAGATACCCTTTCCATTGACACA
genomic: GACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAggtaattttt ... ttcatgcacaGCCAAGATACCCTTTCCATTGACACA
EST: gi|58018272|gb|CX705014.1|CX705014
EST:     AGACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCA                         GCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAAT
genomic: AGACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAggtaattttt ... ttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAAT
EST: gi|209715079|gb|BW677122.1|BW677122
EST:     GATTTGTAGCA                         GCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAAT
genomic: GATTTGTAGCAggtaattttt ... ttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAAT
EST: gi|17518879|gb|BM187921.1|BM187921
EST:     GACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCA                         GCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAAT
genomic: GACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAggtaattttt ... ttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAAT
EST: gi|209729539|gb|BW651866.1|BW651866
EST:     GACTC-TACTTTTGCTGGGGTG-ACTTTTTCTTTTCTGGA-TTGTAGCA                         GCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAAT
genomic: GACTCTTACTTTTGCTTGGGTGAACTTTTTCTTTTCTGGATTTGTAGCAggtaattttt ... ttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattcattacttttactatttacctcttgaaaatgtttaaaactttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAATGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT
                                           ctttcat  CT-rich tract
      attacttttactattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catacatgtgttgacttatgatagtcatctgcttggcacaaccttggattcattacttttactatttacctcttgaaaatgtttaaaactttcatgcacaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAATGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT

catacat
- - - - tgttgac
- - - - - - - - - - - - -catctgc
- - - - - - - - - - - - - - - - - - cacaacc