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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgaatttgttcttttaaaggcaaaatatatattcattgtgtcatcatcactggtttatagttatgagtatgatatcaatttacttgtaaactttccagGTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATATTGTGTATGTAATTGAAGGGGGAGCCGGAACTTACAGTGGAAAACCCAGA

Basic information

species Glycine max
transcript GLYMA11G11370.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11370.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 6
tttgaatttgttcttttaaaggcaaaatatatattcattgtgtcatcatcactggtttatagttatgagtatgatatcaatttacttgtaaactttccagGTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATATTGTGTATGTAATTGAAGGGGGAGCCGGAACTTACAGTGGAAAACCCAGA
                     | ||  | ||| | || | |    | | || || |  ||    ||| |||  |   |  |  | || |||      |||||||||||| ||||||||||| ||||||| |||  |||| || ||||||  |||||| |  ||||||||||| || |||||||||| ||| || || || 
---------------------gtaagttgtat-tacactataa-gttaccagtgatcaatctagatg-gtacaactcc--tgaaattataagtaccgcagGTTGGATGGGGAGCATGTTGTGTTTGGCAGGGTGATTCAGGGAATGGATTATGTGTACGCCATTGAAGGGGGTGCTGGAACTTACAATGGCAAGCCTAGG

upper sequence: GLYMA11G11370.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G34960.1 (Arabidopsis thaliana), 3'ss of exon 5
tttgaatttgttcttttaaaggcaaaatatatattcattgtgtcatcatcactggtttatagttatgagtatgatatcaatttacttgtaaact---ttccagGTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATATTGTGTATGTAATTGAAGGGGGAGCCGGAACTTACAGTGGAAAACCCAGA
     | |    | |  |     || | ||    | ||  |||     ||| || |  ||   ||  ||    || |  ||     || |||||   || ||||||||| ||||| ||||| || || || |||||  | ||||| ||||| | ||| |  |  |||||||| ||||| |||||||||||||| |||||||| 
---agaataacacgtgaattcaaaacacatgagataatcttgtggatttcagtgttgaatttgtaaaaggtaaattttgatgattgtgaaaactgtgttgcagGTTGGAAGGAGAACATGTGGTGTTGGGAAAGGTGATACAAGGAATGGACAATGTATTCGCCATTGAAGGTGGAGCTGGAACTTACAGTGGCAAACCCAGG

upper sequence: GLYMA11G11370.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 6
tttgaatttgttcttttaaaggcaaaatatatattcattgtgtcatcatc-actggtttatagttatgagtatgatatcaatttacttgtaaa-ctttccagGTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATATTGTGTATGTAATTGAAGGGGGAGCCGGAACTTACAGTGGAAAACCCAGA
 |||   |   |  | || |    |||  | |    |     | || ||| ||  ||  ||  |  | |  |  | |  ||| | | | |||| |||  |||||||||||| ||||||||||| || ||||||||| ||||||||||||| ||||| ||   ||| ||||| ||||| ||||| |||| |||||||||||| 
gttg--ctccatgctctagatatgaaacttctgcgtacaagttaatgatctacatgtagatgttccttaccagtaaaagaatatccatttaaaacttggcagGTTGGATGGGGAGCATGTTGTATTGGGCAAGGTTATTCAAGGCATGGACATTGTCTACACAATAGAAGGTGGAGCTGGAACCTACAATGGAAAACCCAGG

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|213603289|gb|DB981946.1|DB981946
EST:     TCCAATGGCTCACAGTTTTTCCTTACTACAGTGAAGGCCAGATG                         GTTGGATGGAGAGCATGTGGTCTTTGGCAAGGTTGTTCAAGGCATGGATAT
genomic: TCCAATGGCTCACAGTTTTTCCTTACCACAGTGAAGGCCAGATGgtaagttatt ... aactttccagGTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATAT
EST: gi|151409712|gb|EV279520.1|EV279520
EST:     CCTGATTCCAATGGCTCACAGTTTTTCCTTACCACAGTGAAAGCCAGATG                         GTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATAT
genomic: CCTGATTCCAATGGCTCACAGTTTTTCCTTACCACAGTGAAGGCCAGATGgtaagttatt ... aactttccagGTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATAT
EST: gi|192301026|gb|FG987981.1|FG987981
EST:     CCTGATTCCAATGGCTCACAGTTTTTCCTTACCACAGTGAAGGCCAGATG                         GTTGGATGGAGAGCATGTTGTCTTTGG
genomic: CCTGATTCCAATGGCTCACAGTTTTTCCTTACCACAGTGAAGGCCAGATGgtaagttatt ... aactttccagGTTGGATGGAGAGCATGTTGTCTTTGG
EST: gi|163921467|gb|EH038979.1|EH038979
EST:     CCTGATACCAATGGCTCACAGTTTTTCCTTACCACAGTGAAGGCCAGATG                         GTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATAT
genomic: CCTGATTCCAATGGCTCACAGTTTTTCCTTACCACAGTGAAGGCCAGATGgtaagttatt ... aactttccagGTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATAT
EST: gi|151406317|gb|EV276132.1|EV276132
EST:     CCTGATTCCAATGGCTCACAGTTTTTCCTTACCACAGTGAAGGCCAGATG                         GTTGGATGGAGAGCATGTTGTCTTTGGGCAAGGTTGTTCAAAGCATGGATA
genomic: CCTGATTCCAATGGCTCACAGTTTTTCCTTACCACAGTGAAGGCCAGATGgtaagttatt ... aactttccagGTTGGATGGAGAGCATGTTGTCTTTGG-CAAGGTTGTTCAAGGCATGGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcactggtttatagttatgagtatgatatcaatttacttgtaaactttccagGTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATATTGTGTATGTAATTGAAGGGGGAGCCGGAACTTACAGTGGAAAACCCAGA
                                               ctttcc  CT-rich tract
                        tatgatatcaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgaatttgttcttttaaaggcaaaatatatattcattgtgtcatcatcactggtttatagttatgagtatgatatcaatttacttgtaaactttccagGTTGGATGGAGAGCATGTTGTCTTTGGCAAGGTTGTTCAAGGCATGGATATTGTGTATGTAATTGAAGGGGGAGCCGGAACTTACAGTGGAAAACCCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - tgtcatc
- - - - - - - - - - - - - - - - - - - - - - - - - actggtt