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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGAATTGGTTTATATGCAGCTGCTAACAGTCTCTACAACGTTGAAGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaaaaattgaaaacggtttgctgtttactgcattggagtgcttgatgattgttactcggttatgattgtggcagtctttgtg...

Basic information

species Glycine max
transcript GLYMA12G33520.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 2
TGGTGGAATTGGTTTATATGCAGCTGCTAACAGTCTCTACAACGTTGAAGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaaaaattgaaaacggtttgctgtttactgcattggagtgcttgatgattgttact--cggttatga--ttgtggcagtctttgtg
||||||  ||||| | ||||  ||| |  ||||||||||||| ||||||||||| || ||||||||  | ||||| ||| |||| ||| | ||||| ||||||| |   ||       |||   |||       || | | || | |  ||     | |   |||| | ||  |   | || |||  ||  |      |||   
TGGTGGGCTTGGTCTCTATGGTGCTACGCACAGTCTCTACAATGTTGAAGGAGGACATCGAGCCATCATGTTCAATCGTTTAGTCGGTATTAAAGATAAGgttagtcagtgtttcttcaaa---ttgggtctttttggattttcagtaaatgtattttcccaatgagtttttttgctgtttgtgagatttggatgaaattttc-

upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 2
lower sequence: AT2G20530.2 (Arabidopsis thaliana), 5'ss of exon 3
TGGTGGAATTGGTTTATATGCAGCTGCTAACAGTCTCTACAACGTTGAAGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaaaaattgaaaacggtttgctgtttactg-cattggagtgcttgatgattgttactcggttatgattgtggcagtctttgtg-----
||| ||  |  || | || |  ||| |  ||| ||||||||| || || |||||||| ||||||||||| || ||||| || |||||| ||||||||||||||| |   ||    |||||    ||      |  |  |||| || || || || |     || |  | |  |    | |    ||  |  || ||| |       
TGGGGGGCTCAGTCTTTACGGTGCTACGCACACTCTCTACAATGTCGATGGAGGTCATCGAGCCATTGTCTTTAACCGGCTTGTTGGTATCAAAGACAAGgttagtccctgc---aaaaattggtttcttctgaat--ctgtatattgacaatgaatcttgtggttgt-gacatctagctgaagttaggttaggcttagcattact

upper sequence: GLYMA12G33520.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 5'ss of exon 3
TGGTGGAATTGGTTTATATGCAGCTGCTAACAGTCTCTACAACGTTGAAGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaaaaattgaaaacggtttgctgtttactgcattggagtgcttgatgattgttactcggttatgattgtggcagtctttgtg---
||||||  ||||||| |||| ||||  ||||||||| ||||| ||||| |||||||| || |||||||| || || ||  ||||||||||||| ||||||||| | || |                  |   |   ||   |  | |  |||    |  |||    |  |||   |||| |    ||    |  |||      
TGGTGGGCTTGGTTTGTATGGAGCTATTAACAGTCTGTACAATGTTGAGGGAGGTCATCGGGCCATTGTGTTTAATCGCATAGTTGGTGTCAAGGACAAGgttctcatttccccttggtttcttgcatatgagacctgaaatccattaaatta---tttttgtctctgcttatatggttttttgggtaattgcttttagattt

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|20449070|gb|BQ253194.1|BQ253194
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taatgtgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
EST: gi|254329670|gb|GR839223.1|GR839223
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taatgtgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
EST: gi|192329319|gb|FK020238.1|FK020238
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taatgtgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
EST: gi|12497305|gb|BG047500.1|BG047500
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAAC
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taatgtgcagGTCTATCCTGAAGGAAC
EST: gi|151402542|gb|EV272355.1|EV272355
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taatgtgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
EST: gi|298192023|gb|HO036105.1|HO036105
EST:     CGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACACACTTTACGATTCCGTGGTTTGAGAGGCCTGTT
genomic: CGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taatgtgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
EST: gi|192303429|gb|FG997459.1|FG997459
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taatgtgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
EST: gi|151412668|gb|EV282480.1|EV282480
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taatgtgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
EST: gi|151413130|gb|EV282938.1|EV282938
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taatgtgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGAATTGGTTTATATGCAGCTGCTAACAGTCTCTACAACGTTGAAGGAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatatgaagaaaaaaaaaattgaaaacggtttgctgtttactgcattggagtgcttgatgattgttactcggttatgattgtggcagtctttgtg

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