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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttagaacttcttttttcatattcatgttattatttcttcattgtaaataaattgtagtggccagaattttcttgtaatgtgagcatttttttagtagGTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTTTACAAGGAGGCTGCAAATATTGAGGCTTTTAGGAGATATTTAGAAACAA

Basic information

species Glycine max
transcript GLYMA14G36520.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36520.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G05200.1 (Arabidopsis thaliana), 3'ss of exon 6
aacttagaacttcttttttcatattcatgttattatttcttcattgtaaataaattgtagtggcc---agaattttcttgtaatgtgagcatttttttagtagGTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTTTACAAGGAGGCTGCAAATATTGAGGCTTTTAGGAGATATTTAGAAACAA
| || || || |||| | | ||| ||| || | || ||| || | || | | |||||||| |||||||||||||| |||||||| |||||||||||||| || || | ||||||||| ||| |||||| | |||| ||||||| | ||||| |
-------------------------------gtaatctcctc--tgtatttgatttgcagtcgctcttaagatactctctaaacaatattatcctatggatagGTTGGAATTGTCAAAGATATTCGTGAGTCAATGCTTGAAGAAGTAGATTTCAATAAGGAGGCTCAAAACATTGAGTCATTTAAGAGATATCTTGAAACCA

upper sequence: GLYMA14G36520.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g03210.t01 (Vitis vinifera), 3'ss of exon 6
--aacttagaacttcttttttcatattcatgttattatttcttcattgtaaataaattgtagtggccagaattttct--tgtaatgtgagcatttttttagtagGTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTTTACAAGGAGGCTGCAAATATTGAGGCTTTTAGGAGATATTTAGAAACAA
| ||||| || || | | | | || |||| || || |||| | |||| |||| ||||| | |||||| ||| ||| |||||||||||||||| ||||| ||| | || || |||||||||||||||||||| | |||||||||||||||||||| || |||||||||||||||||| |||
aacatttagagatttttgtcatgcaccattcatgttctttcatcttttgaaatga----cgatggctagaagtttctattataatgtatacatcctttcagtagGTTGGTATTGTGAAAGACATAAGGGAATCAATGCTTGAAGAAGTTGACTTCAATAAGGAGGCTGCAAATATTGAAGCCTTTAGGAGATATTTAGAAGCAA
















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|120494303|gb|EH222470.1|EH222470
EST:     TTGCTAGGATATTGGAGTTCTTGAGTCCTGAAATAAGCCGAACATCACTG                         GTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTT
genomic: TTGCTAGGATATTGGAGTTCTTGAGTCCTGAAATAAGCCGAACATCACTGgtaagctgta ... tttttagtagGTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTT
EST: gi|17519076|gb|BM188118.1|BM188118
EST:     TTGCTAGGATATTGGAGTTCTTGAGTCCTGAAATAAGCCGAACATCACTG                         GTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTT
genomic: TTGCTAGGATATTGGAGTTCTTGAGTCCTGAAATAAGCCGAACATCACTGgtaagctgta ... tttttagtagGTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTT
EST: gi|20498291|gb|BQ273221.1|BQ273221
EST:     TTGAGTCCTGAAATAAGCCGAACATCACTG                         GTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTT
genomic: TTGAGTCCTGAAATAAGCCGAACATCACTGgtaagctgta ... tttttagtagGTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTT
EST: gi|7690969|gb|AW759104.1|AW759104
EST:     TTGCTAGGATATTGGAGTTCTTGAGTCCTGAAATAAGCCGAACATCACTG                         T
genomic: TTGCTAGGATATTGGAGTTCTTGAGTCCTGAAATAAGCCGAACATCACTGgtaagctgta ... tttttagtag-
EST: gi|7690969|gb|AW759104.1|AW759104
EST:     TTGCTAGGATATTGGAGTTCTTGAGTCCTGAAATAAGCCGAACATCACTG                         T
genomic: TTGCTAGGATATTGGAGTTCTTGAGTCCTGAAATAAGCCGAACATCACTGgtaagctgta ... tttttagtag-
EST: gi|7690969|gb|AW759104.1|AW759104
EST:     TTGCTAGGATATTGGAGTTCTTGAGTCCTGAAATAAGCCGAACATCACTG                         T
genomic: TTGCTAGGATATTGGAGTTCTTGAGTCCTGAAATAAGCCGAACATCACTGgtaagctgta ... tttttagtag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaataaattgtagtggccagaattttcttgtaatgtgagcatttttttagtagGTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTTTACAAGGAGGCTGCAAATATTGAGGCTTTTAGGAGATATTTAGAAACAA
                                         cattttttt  CT-rich tract
 aattttcttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttagaacttcttttttcatattcatgttattatttcttcattgtaaataaattgtagtggccagaattttcttgtaatgtgagcatttttttagtagGTTGGTATTGTCAAAGATATACGTGAGTCTATGCTTGAAGAAGTTGACTTTTACAAGGAGGCTGCAAATATTGAGGCTTTTAGGAGATATTTAGAAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - tcatgtt
- - - - - - - - - - - - - - - - - - - cttcatt
- - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtagtgg