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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaatatttggagtaaatattttctcatctcttacatcacatgctttttgtttcatagaatttctgcttatgttgttgggtggtggtgttgactt...

Basic information

species Glycine max
transcript GLYMA06G47830.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G47830.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os08g42690.1 (Oryza sativa), 5'ss of exon 6
GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaatat-ttggagtaaatattttctcatctcttacat-cacatgctttttgtttcatagaatttctgcttatgttgttgggtggtggt--gttgactt
||  |||| || ||  |||    ||| || ||||| || ||||||||||||||||| ||||  || || || ||||| ||||| ||||| ||||||||| | | |  |  | ||||     |  ||  |   || |   || |       |  |  | || | || ||  | |      ||     |  ||||    
GGTCTGAAGAAGGCTTTAGATGGTGGAGCAGACAAAGACGAAGAAGATTCAGAGGGCAGAAGGGCCTTACACTTTGCATGTGGGTATGGGGAGgtatgcaagtctgcttaactaaacccaatgacaattgaaacctgtgcaagtagaaaatgccgaataaatactactattatctactagtacctatttgttg----

upper sequence: GLYMA06G47830.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM5G800734_T02 (Zea mays), 5'ss of exon 6
GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaat--atttggagtaaatattttctcatctcttacatcacatgctttttgtttcatagaatttctgcttatgttgttgggtggtggtgttgactt----
|| ||||| || ||  |||    ||| || |||||||||||||||||| | |||||||||   ||||| |||||||| ||||| ||||| |||||| |  |||   ||     |   ||       ||   |||||  ||||||   |  | |    |||| ||  || |||  |  ||  |       |   ||    
GGTTTGAAGAAAGCTTTAGAAGGTGGAGCAGACAAGGATGAAGAAGATGCCGAGGGAAGACGGGCTTTACATTTTGCATGTGGCTATGGTGAGgtaagtgaatctgttatactttgttaaacggaaatagattacacaacatgcagctaatgt----gaatatc--ctgatgcagcaggacgaccaccatttgttatgt

upper sequence: GLYMA06G47830.1 (Glycine max), 5'ss of exon 7
lower sequence: AC215244.3_FGT002 (Zea mays), 5'ss of exon 6
GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaatatttggag---taaatattttctcatctcttacat--cacatgctttttgtttcatagaatttctgcttatgttgttgggtggtggtgttgactt
||  | || || |||||||    ||| || ||||||||||||||||| || ||||||||||  || || |||||||| ||||| || || |||||||||  || | |  ||   |    | ||    | ||  |  ||  ||   | |           | ||||  |  | ||  |      ||     |       
GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAGgtatgcagatctcttcagccttgttaacttgtggaactaatgaatgccaagcgataccaacacttcaaaattgtttatcatactaccacatgactaggca-----

upper sequence: GLYMA06G47830.1 (Glycine max), 5'ss of exon 7
lower sequence: AT2G17390.1 (Arabidopsis thaliana), 5'ss of exon 7
GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaatatttggagtaaatattttctcatctcttacatcacatgctttttgtttcatagaatttctgcttatgttgttgggtggtggtgttgactt----
|| ||||||  |||  | || |||||||   |||| ||||||||||| || || ||||| ||||||||||||||||| |||||||| |||||||||||  ||  | |  |  |      ||  ||      || |  |    | |   | ||| |||||    |       | |    |     | || |||     
GGTTTGAAAGCTGCCTTGGCATCTGGTGGGAACAAAGATGAAGAAGACTCTGAAGGAAGGACTGCTTTGCATTTTGCATGTGGATACGGCGAGgtatgtcaacgtctcaacaag---ccttaacaaaaaaaac-tgtcgaaatgtcactatcacagaatcatggaaggcagtatatactaccaatatttactagcat

upper sequence: GLYMA06G47830.1 (Glycine max), 5'ss of exon 7
lower sequence: AT4G35450.5 (Arabidopsis thaliana), 5'ss of exon 7
GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaatatttgg---agtaaatattttctcatctcttacatcacatgctttttgtttcatagaatttctgcttatgttgttgggtggtggtgttgactt
|| ||||||  |||  | || ||||||| | |||| |||||||||||||| || ||||| || || ||||||||||| |||||||| |||||||||||| | | | |     | | |      |   || |      | | ||| || |  |||  |  | |  ||| | | |||   |  |  |  |  | | | 
GGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCTGAAGGAAGGACAGCATTGCATTTTGCTTGTGGATACGGCGAGgtatgcaattctcttatcaattcacggcaattaaatattcggatttagatggttctc-tttttttcagtagctg-tgaagttaa-gaatctttataatcattc

upper sequence: GLYMA06G47830.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv03s0038g04270.t01 (Vitis vinifera), 5'ss of exon 7
GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaatatttggagtaaatattttctcatctcttacatcacatgctttttgtttcatagaatttctgcttatgttgttgggtggtggtg--ttgactt---
|| ||||| |||||||| ||||||||||| ||||| ||||||||||||||||||||||| |||||  ||||||| || ||||| ||||| |||||||| || |      | |  || |||  |    ||||| || ||||   || |    ||  | ||||        || ||  ||   || ||  || |  |   
GGTTTGAAGAATGCACTTGCCTCTGGTGCCGACAAAGATGAAGAAGATTCAGAGGGAAGGACTGCACTGCATTTCGCATGTGGGTATGGTGAGgtatgatagt-ccaaaaatggatctttctt---ttcttatat-acatatattcttgagcaatggattttactcagagtagtatgggcatgatgatttaatctaag

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|6726653|gb|AW311007.1|AW311007
EST:     AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG                         GTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
genomic: AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaat ... atcatttcagGTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
EST: gi|151401062|gb|EV270876.1|EV270876
EST:     AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG                         GTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
genomic: AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaat ... atcatttcagGTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
EST: gi|254335877|gb|GR847405.1|GR847405
EST:     AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG                         GTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
genomic: AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaat ... atcatttcagGTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
EST: gi|254335741|gb|GR847269.1|GR847269
EST:     AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG                         GTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
genomic: AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaat ... atcatttcagGTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
EST: gi|17152886|gb|BM142819.1|BM142819
EST:     AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG                         GTAAAATGTGCTCAAGTTCTACTCGAGGCTGGAGCAAAAGCGGATGCT
genomic: AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaat ... atcatttcagGTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCT
EST: gi|192309989|gb|FK002513.1|FK002513
EST:     AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG                         GTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
genomic: AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaat ... atcatttcagGTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
EST: gi|254335742|gb|GR847270.1|GR847270
EST:     AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG                         GTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
genomic: AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaat ... atcatttcagGTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
EST: gi|209715175|gb|BW665652.1|BW665652
EST:     CTGTGGATATGGCGAG                         GTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
genomic: CTGTGGATATGGCGAGgtatgctaat ... atcatttcagGTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
EST: gi|21601758|gb|BQ612089.1|BQ612089
EST:     AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAG                         GTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
genomic: AAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaat ... atcatttcagGTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
EST: gi|6726608|gb|AW310962.1|AW310962
EST:     AGATTCAGAGGGAAGAACTGC-TTGCATTTTTGCCTGTGGATATGGCGAG                         GTAANATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG
genomic: AGATTCAGAGGGAAGAACTGCTTTGCA-TTTTGCCTGTGGATATGGCGAGgtatgctaat ... atcatttcagGTAAAATGTGCTCAAGTTCTCCTCGAGGCTGGAGCAAAAGTGGATGCTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTTGAAAAATGCACTAGCCTCTGGTGCTGACAAGGATGAAGAAGATTCAGAGGGAAGAACTGCTTTGCATTTTGCCTGTGGATATGGCGAGgtatgctaatatttggagtaaatattttctcatctcttacatcacatgctttttgtttcatagaatttctgcttatgttgttgggtggtggtgttgactt

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggtgg