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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgcttatcaaaatgttcttacttgaaactttacacttttggtaatttccttgactgttttcctatgaccaaatgatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA

Basic information

species Glycine max
transcript GLYMA08G09180.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G088974_T01 (Zea mays), 3'ss of exon 5
------------gttggtgcttatca-aaatgttcttacttgaaactttac--acttttggtaatttccttgactg-----ttttcctatgaccaaatgatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA
             |||||      ||  ||| |   |||||  |  || |   | ||   ||   || ||| | ||     | || || | || || | ||  |  || |   ||| ||    |   |||| ||||  || || ||||| |||||||| ||||||||| ||||||||   | ||| ||| |||||||||||||||| 
gtaatgaatgcttttggtttgggccatgaatataactacttccagtttcaaggatttcaagttcatttcttcattgaatattctttcttttactaacttatattttagATTAGTGTTTGCTCCACCAATAATCCAGTTGACGCCTCATTCTTTGAATCCTTTGAAGCATCACACTCCAAGCGTGATTTAACTAGCTCCATTGCAGAG

upper sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 5
gttggtgcttatcaaaatgttcttacttgaaactttacacttttggtaatttccttgactgttttcctatgaccaaatgatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA
|||| | || ||  || | || | | | || | || |     || | |  ||    |  ||||||           ||   | |  ||||||||||| | |  ||||| ||||| |||||||||||||| |||||||| |||||||||||||||||    |||||||| ||||||||||| ||| | 
gttgatactaatgcaattatt-tcaatggatatttca-----tttgaacattagaagcttgtttttgatacttttgattgccctttagGTGCATGTCAGCGCCATTGAAAACCCCGAGGAAGCATCATTCTTTGAATCATTTGAAGCAGCACACTCAAAGCATGACTTGTCTAGCTCCATAGCAAAG
















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|13311617|gb|BG405268.1|BG405268
EST:     TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGG                         GTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT
genomic: TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGGgttggtgctt ... gatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT
EST: gi|12497023|gb|BG047358.1|BG047358
EST:     TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGG                         GTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT
genomic: TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGGgttggtgctt ... gatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT
EST: gi|207701824|gb|GD682495.1|GD682495
EST:     TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGG                         GTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT
genomic: TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGGgttggtgctt ... gatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT
EST: gi|192311655|gb|FK004874.1|FK004874
EST:     TTGGTGATGGAGCATATATGCAAGCACTGGGTGGTTCTACACAAACTAGG                         GTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTT-GA-TCT
genomic: TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGGgttggtgctt ... gatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT
EST: gi|51344888|gb|CO985621.1|CO985621
EST:     TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGG                         GTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT
genomic: TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGGgttggtgctt ... gatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT
EST: gi|6725411|gb|AW309810.1|AW309810
EST:     TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGG                         GTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT
genomic: TTGGTGATGGAACATATATGCAAGCACTGGGTGGTTCTACACAAACTAGGgttggtgctt ... gatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacacttttggtaatttccttgactgttttcctatgaccaaatgatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA
                   ccttgac  putative branch site (score: 4)
             taattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtgcttatcaaaatgttcttacttgaaactttacacttttggtaatttccttgactgttttcctatgaccaaatgatcatccagGTGCATGTCTGTGATATTGATAACCCAGAGGAAGCATCATTTTTTGAATCTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC