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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattcttgattttgttatattatataccgaatggacgatcagatcttagttgatttattgggcagcatattctctttttacaattttcaatattttgtattttcggtgcag

Basic information

species Glycine max
transcript GLYMA16G33380.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os02g14929.1 (Oryza sativa), 5'ss of exon 5
TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttctgcatgatttaata-gcaaaattcttgattttgttatattatataccgaatggacgatcagatcttagttgatttattgggcagcatattctctttttacaattttcaatattttgtattttcggtgcag
|||||||||||  |||| ||||| || || |||||||| |||||||| || |||||||| ||  |||||||||||    |   || |    || ||  | ||   ||      |   ||| |||  ||| |  |    |||| |    |        |||  |   ||   |||                                   
TCTATGATTGAGCTAAGCCGCACACAGGATGAAGAAGTAGGAGATGGCACGACATCTGTTATTGTTCTTGgtatgccgtttt-tggtcccttatgcttattttaagagaccagttggtta-atattgaacgcgcag--agatgtagcctagagggggggggggtgaataggctt-----------------------------------

upper sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 5'ss of exon 5
TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattcttgattttgttatattatataccgaatggacgatcagatcttagttgatttattgggcagcatattctctttttacaattttcaatattttgtattttcggtgcag
|||||||||||  |||| || || || || ||||||||||| ||||| ||||||||||||||  || | ||||||| |   | ||||| | |  ||   |  || | |||  ||| ||| ||  |  |||   ||||  | |     |    ||| | |   ||| |  |  |  |  || |                          
TCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAACATCTGTCATTGTTTTAGgtatgtgttccc-tgattcatt--cagtttcattcagttt--tat-ttaaatgtcatatga--gatcgcaac---actaggatatcgtg--acatctctttctggtcgaacta-------------------------

upper sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G175510_T02 (Zea mays), 5'ss of exon 5
TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattcttgattttgttatattatataccgaatggacgatcagatcttagttgatttattgggcagcatattctctttttacaattttcaatattttgtattttcggtgcag
|||||||||||| ||||||| || ||||| ||||||||||| ||||| || |||||||||||  |||| ||||||  | |   |  | | | |      ||    | ||  | |   |         |   || |    ||   | || ||||       |  | |     |                                    
TCTATGATTGAACTAAGTCGTACACAAGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgcatattttt--tgtgacatttgttttgggaagttgatgactatgagcctatgacaaacaacagcattgcaatttatttgcatcaaactaaaacagtt------------------------------------

upper sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G069765_T02 (Zea mays), 5'ss of exon 5
TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattcttgattttgttatattatataccgaatggacgatcagatcttagttgatttattgggcagcatattctctttttacaattttcaatattttgtattttcggtgcag
|||||||| ||| ||||||| || || || ||||||||||| ||||| || |||||||||||  |||| ||||||  |       ||||  | |  |||||  |  ||| |  |  ||     |      ||  ||||  |   | || ||||     ||| || | |       | | |||| ||                      
TCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGgtatgggt-------atttttttgtgaaatttct--tttcggaaagttgatggctatgatgaacatca--ttgcaatttattt-----gcatcaaactaaagcagtgctatttgca----------------------

upper sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 5'ss of exon 5
TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattcttgattttgttatattatataccgaatggacgatcagatcttagttgatttattgggcagcatattctctttttacaattttcaatattttgtattttcggtgcag
|| |||||||||||||| ||||| ||||| ||||||||||| |||||||| || || |||||  |||||||||  | |||   | |  |  ||| | |||| ||  ||    || |  ||  |    ||      ||   | | |  || |||  ||||  ||||||    ||  |   |                            
TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTGgtacatctct---taaacttgtag-ataattattctttcgaata-acaatgaattatat---tattcttgtttca--tgttttgatggggtgcatatatcattaatgtga----------------------------

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|16284063|gb|BI945885.1|BI945885
EST:     CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
genomic: CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttct ... ttcggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
EST: gi|16276828|gb|BI942066.1|BI942066
EST:     CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
genomic: CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttct ... ttcggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
EST: gi|16281961|gb|BI944761.1|BI944761
EST:     CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGAT
genomic: CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttct ... ttcggtgcagCTGGTGAGATGCTTCATGTCGCCGAT
EST: gi|193636212|gb|FK580749.1|FK580749
EST:     CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCG
genomic: CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttct ... ttcggtgcagCTGGTGAGATGCTTCATGTCGCCG
EST: gi|16278542|gb|BI942959.1|BI942959
EST:     CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATGCACCCTA
genomic: CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttct ... ttcggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
EST: gi|24206236|gb|BU965489.1|BU965489
EST:     CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCGGATGCATTCATTGACAAAATTCACCCTA
genomic: CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttct ... ttcggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA
EST: gi|162286128|gb|FC456630.1|FC456630
EST:     CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG                         CTGGTGAGATGCTTCATGTCGCGGATGCATTCATTGACAAAATTCACCCTA
genomic: CACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttct ... ttcggtgcagCTGGTGAGATGCTTCATGTCGCCGATGCATTCATTGACAAAATTCACCCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTGgtatgtttctgcatgatttaatagcaaaattcttgattttgttatattatataccgaatggacgatcagatcttagttgatttattgggcagcatattctctttttacaattttcaatattttgtattttcggtgcag

- - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - GATGGA