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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcattgttgttgttgttattgtcgtttttgagtggcgtaattggattgttgtgtcacttgtatgtgtgttttgagggttgtgccttgtgtgtttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATT

Basic information

species Glycine max
transcript GLYMA09G28040.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28040.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G25370.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagttcattgttgttgttgttattgtcgtttttgagtggcgtaattggattgttgtgtcacttgtatgtgtg---ttttgagggttgtgccttgtgtgtttggttc-agGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATT
              ||   | | | |     ||  |  | |   |||| | |  ||||    ||| || || ||   | |||||| || |   ||   |||||| ||  || ||||||| ||| |||||||| ||   ||||||||| |||||||| || |||||||||||||||||||  || || ||||| || ||||||||||| |||
--------------gtgagtctcactccaaattacgtatag---aatttg-taattgtagagcttatacgtttgaattgttgaggttttttttttaattgtttgattttagATGGTCGGCGAGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATT

upper sequence: GLYMA09G28040.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0022g01840.t01 (Vitis vinifera), 3'ss of exon 2
gtgagttcattgttgttgttgttattgtcgtttttgagtggcgtaattggattgttgtgtcacttgtatgtgtgttttgagggttgtgccttgtgtgtttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATT
   | |  | | |||      ||||| |  | ||||     | || ||   |||     |     || | |     ||        ||  | |    |   ||| || |||||||  ||||| ||||| || | | | |||| |||||||||||| |||||||| ||||| ||||| || |||||||||||  |||| ||||| || 
---aatataatattgaaaac-ttatttt--tctttgttctccttatttttcttggcaactagacagtgt-tagaacttactttaaatgtatgggaaatggtgtttagATGGTCGGCCAGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATC
















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|14990401|gb|BI316074.1|BI316074
EST:     GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAA                         GTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
genomic: GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAAgtgagttcat ... tttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
EST: gi|4284742|gb|AI440819.1|AI440819
EST:     GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAA                         GTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
genomic: GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAAgtgagttcat ... tttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
EST: gi|6848038|gb|AW350328.1|AW350328
EST:     GAAACCCCNTNCGGATACGCCCGATAAAACCCCAAA                         GTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
genomic: GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAAgtgagttcat ... tttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
EST: gi|298183306|gb|HO028519.1|HO028519
EST:     GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAA                         GTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
genomic: GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAAgtgagttcat ... tttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
EST: gi|7589480|gb|AW705253.1|AW705253
EST:     GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAA                         GTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
genomic: GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAAgtgagttcat ... tttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
EST: gi|23064459|gb|BU579232.1|BU579232
EST:     GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAA                         GTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
genomic: GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAAgtgagttcat ... tttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
EST: gi|24135410|gb|BU925920.1|BU925920
EST:     GAAACCACTTTCGGATACGCCCGATAAAACCCCAAA                         GTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG
genomic: GAAACCCCTTTCGGATACGCCCGATAAAACCCCAAAgtgagttcat ... tttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcattgttgttgttgttattgtcgtttttgagtggcgtaattggattgttgtgtcacttgtatgtgtgttttgagggttgtgccttgtgtgtttggttcagGTGGTCGGAGAGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA