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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatctgccttatatctcaaacttctgttgaaattttgaaatctaagaagcaaactatttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTTCTT

Basic information

species Glycine max
transcript GLYMA19G27800.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g32490.1 (Oryza sativa), 3'ss of exon 8
------------------------------------gtagatc-tgccttatatctcaaacttctg--ttgaaattttgaa--atctaagaagcaaactat---ttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTTCTT
                                     ||  |  ||    || | | || ||||||  |||  |   ||||   | |         | | |   ||   |||| | | || ||  || | ||    || |||||||||| ||| ||||||||||| |||||||||||||||||||||||| ||||||| 
gtatcgctctgttatacatgtattcatctaaccatcctaagtaatgtaacatttttaaatcttctggcttggcacactgaatactttcttgtttcgattgtaaattaaaagGAAATCAAGCACAGAAGCCAAGCCGGATCGAGGAATATTTGTAAAGCATTTCAAGAACATTCCAATGGCTGATATGGAATTAGTTCTG

upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os12g29550.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------------gtagatctgccttatatctcaaacttctgttgaaatt---ttgaaatctaagaagcaaactat-ttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTTCTT
                                              |  |    ||| || | |  || | ||| || | |    |||    ||    |  |   ||| | | |||||| ||  | || ||  | ||    || |||||||||| ||| ||||||||||| || || ||||||||||| |||||||| ||||||
gtaactttgaccctttgatattttgtttagccaatctccacattcatgaaggatcctaat-tttagaagtgctgatgtagtacaattggttccttccgatgattgtatatgtgcagGAGGGCAGGTACTAAGACTAAGCCTGATCGAGGAATATTTGTAAAGCATTTCAAGAATATCCCAATGGCTGACATGGAAATTGTTCTT

upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G011136_T01 (Zea mays), 3'ss of exon 8
------------------------------------gtagatctgccttatatctcaaacttctgttgaaattttgaaatctaagaagcaaactatttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTTCTT
                                       |||   |  |     |   | |  || || | || |   ||||     |        | | |||||| ||  | || ||  |  ||   || || ||||||| ||| ||||| ||||| || || ||||||||||| |||||||| ||||||
gtagattcaatgttctgattgctcaaccttcaaattcatgatggactctggtgttattattcttgatgcagttatattatctggcctgattgtgtatgtacagGAGGGCTGGTACAAAGACTGAACCTGATCGGGGAATATTTGTAAAGCACTTCAAGAATATCCCAATGGCTGACATGGAAATTGTTCTT

upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G19340.1 (Arabidopsis thaliana), 3'ss of exon 8
-----gtagatctgccttatatctcaaacttctgtt-gaaattttg-aaatctaagaagcaaact-----------atttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTTCTT
     ||| || |   |  | | |||    | |||| | || ||||  ||  |  |   ||| ||           || || |||  |||| ||  | ||| ||||   |||||||||||| || || |||||||||||||||||||| |||||||| ||||| || || |||
gtaaggtatatgtatgtcttgtttcagctatttgtttgtaactttgtgaacttgtggttcaagcttgtggtttatgatgttgcagACGAGCTAGCTCTAAAACAAATCTAGAACGAGGAATCTACGTTAAGCATTTCAAAAACATTCCTATGGCTGACATGGAGATTGTGCTT

upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------gtagatctgccttatatctcaaacttctgttgaaatt------ttgaaatctaagaag-caaactatttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTTCTT
                          |     |   ||||    | |||   |  | || | |      |||  |||||| |||  |    | ||| |||| | ||  | ||   | |||||  ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| || 
aaattaccaaggtccttgtctgaagtgctctccgatcttagcatttaaaacaccatggagaataattcattggcatctaacaagataggtgactttgcagGCGGGCATGTACGGCAGCAAAACCAGAGCGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTCCTG

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|13481712|gb|BG511055.1|BG511055
EST:     AAGACCTTAATCCAAG-ACCAACATTTGATAGGATAATTGTTGTCTACAG                         GAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTT
genomic: AAGACCTTAATCCAAGAACCAACATTTGATAGGATAATTGTTGTCTACAGgtagatctgc ... tatttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTT
EST: gi|207705325|gb|GD687357.1|GD687357
EST:     AAGACCTTAATCCAAGAACCAACATTTGATAGGATAATTGTTGTCTACAG                         GAGAGCCGGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTT
genomic: AAGACCTTAATCCAAGAACCAACATTTGATAGGATAATTGTTGTCTACAGgtagatctgc ... tatttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatctcaaacttctgttgaaattttgaaatctaagaagcaaactatttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTTCTT
                                            ctatttttc  CT-rich tract
                    aaattttgaaatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatctgccttatatctcaaacttctgttgaaattttgaaatctaagaagcaaactatttttcagGAGAGCCAGAACCAAATCAAAAGAAGAACGAGGAATATATGTGAAGCATTTCAAAAACATTCCAATGGCTGATATGGAAATAGTTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT