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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGACCGTTTGCTTGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgtagccttatagtcttatattgtaaatacgttctaagttgcatgcaatgcattatttgtatggtttcacatgaatttagttttctgatcctt...

Basic information

species Glycine max
transcript GLYMA17G33690.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G33690.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 4
-GATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGACCGTTTGCTTGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgtagccttatagtcttatattgtaaatacgttctaagttgcatgcaatgcattatttgta---tggtttcacatgaat--ttagttttctgatcctt
   || |||||||||||| || || ||  | ||||||||||||||| |  |||||||||| ||||| ||||| || ||| | ||||||||||| |||||||||||   ||     | |  ||   || |  | |     |||   |||||||  | |  ||  ||| |    |  | |  |||||    ||| |||| |  |  ||
CAGTG-TGGATCAACTGCATCAACCGCTGTCCTTGTTGGTGACCGTCTCTTTGTTGCAAACGTTGGAGACTCTAGGGCTATCATATGCAGGGGGGGAAATGgtaa--ttgacagttcactgtaccatctcttcagc---ttcctggttgcatttacttgatactttctgactttatatagcatgacacattattttttttcttttt

upper sequence: GLYMA17G33690.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os06g48300.1 (Oryza sativa), 5'ss of exon 4
GATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGACCGTTTGCTTGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgtagccttatagtcttatattgtaaatacgttctaagttgcatgcaatgcattatttgtatggtttcacatgaatttagttttctgatcctt--
||||| || || ||||| |||||||| ||||| || || |||||| |||| |||||||||||||| || || || ||||| || || || || ||| ||||||||  |     | | |    | || ||     |||    |  ||||     |  || | | |  |     |  |||||  |||       ||  |  |  
GATGCAGGGTCGACTGCCTCCACTGCAATTCTCGTAGGCGACCGTCTGCTCGTTGCAAATGTTGGAGATTCTAGGGCTGTCATTTGTAGAGGAGGAGATGgtaagattaagaacatttcaattcatgtttactttactgatt--gttgggcagatagcgtaagtgcttcacctgtacatgtttttcaaccaatgtcctgtcc

upper sequence: GLYMA17G33690.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G166035_T02 (Zea mays), 5'ss of exon 4
GATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGACCGTTTGCTTGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgtagccttatagtcttatattgtaa-atacgttctaagttgcatgcaatgcattatttg-tatggtttcacatgaatttagttttctgatcctt
|||||||| |||||||| || || || ||| |||| ||||| ||||||||||||||||||||||| || || ||||||||||| |  |  || ||| | ||||||  |   | | ||   |   ||||   |   |   |||  |     |  || || || |     |   ||||    || ||||   |    ||   | 
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGATCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCTGTTATTTCTAAAGGAGGACAGGgtaagtttaccgtcgtaacatggcatatctcagtgtctattcctatacttacaca-tgtatcagaaacttctgtttgctgtgtattttcctggacgagtat-

upper sequence: GLYMA17G33690.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM5G829894_T01 (Zea mays), 5'ss of exon 3
GATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGACCGTTTGCTTGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgtagccttatagtcttatat-tgtaaatacgttctaagttgcatgcaatgcattatttgtatggtttcacatgaatttagttttctgatcctt---
|||||||| |||||||| || || || ||| |||| ||||||||||||||||||||||||||||| || || ||||| ||||| |  |  || ||| | ||||||  | | |  |  ||   | | || | | |||   || |    | | | ||   |||   | | |   ||||| || | | ||   |    ||  |    
GATGCTGGCTCAACTGCCTCAACAGCTATTATTGTAGGTGACCGTTTGCTTGTTGCAAATGTTGGAGATTCTAGAGCCGTTATTTCTAAAGGAGGACAAGgtaagtttctcgt-tggtaacatgacatatctcaatgtcttttcctatacttcca---catgtatcggaaactttcaaattattatatgctgtgtattttcctg

upper sequence: GLYMA17G33690.2 (Glycine max), 5'ss of exon 5
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 5'ss of exon 5
GATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGACCGTTTGCTTGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgtagccttatagtcttatattgtaaatacgttctaagttgcatgcaatgcattatttgtatggtttcacatgaatttagttttctgatcctt-------
|||||||| ||||| || || || |||||  | |||||||||||||| |||||||||||||| |||||||| |||||||| |||||||| ||||| |||||||| |||       |  | | ||||  |  || |   || |  |  |  |  |||| |    ||  | ||||  | |  |    |        ||           
GATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGACCGTTTACTTGTTGCAAATGTAGGGGACTCTAGAGCTGTAATATGCAGAGGTGGCAATGgtaatgct-----tgttcatttttattatagaactttttttttgggggatttgaatgga--gattagaaggttgaaaaaaagaaaaaaaaaagaatggagattagaa

upper sequence: GLYMA17G33690.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 5'ss of exon 5
GATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGACCGTTTGCTTGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgtagccttatagtcttatattgtaaatacgttctaagttgcatgcaatgcattatttgtatggtttcacatgaatttagttttctgatcctt---
||||||||||||||||| ||||| || || |||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||| |||||||||  | |||  |   | | |||| ||   ||    || |  |   ||     |  ||  |   | ||  |    | ||    | || | |||   |    
GATGCTGGATCAACTGCCTCCACCGCTATCCTTGTTGGTGACCGTTTGCTGGTTGCAAATGTTGGGGACTCCAGAGCTGTTATCTGCAGGGGTGGTAATGgtaaga-tctagtgtgtcatttttatttttggaaatttttttgtgcatcagagtttctatcgtaattttgaatcttgaagag--catttatatgactttcaaa

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|308098639|gb|HO760380.1|HO760380
EST:     TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATG                         CCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAA
genomic: TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgt ... cctcttctagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGAGGCGAA
EST: gi|10845528|gb|BF071133.1|BF071133
EST:     TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATG                         CCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGAGGCGAA
genomic: TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgt ... cctcttctagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGAGGCGAA
EST: gi|151406983|gb|EV276798.1|EV276798
EST:     TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATG                         CCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGAGGCGAA
genomic: TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgt ... cctcttctagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGAGGCGAA
EST: gi|15662272|gb|BI699643.1|BI699643
EST:     TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATG                         CCATTGCTGTTTCTCGGGATCACAAGCCAGATCAAACTGATGAGAGGCGAA
genomic: TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgt ... cctcttctagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGAGGCGAA
EST: gi|151409117|gb|EV278925.1|EV278925
EST:     TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATG                         CCATTGCTGTTTCTCGAGATCACAAGCCAAACCAAACTGATGAGAGGCGAA
genomic: TGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgt ... cctcttctagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGAGGCGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGACCGTTTGCTTGTTGCAAATGTTGGGGACTCCAGAGCTGTTATATGCAGGGGTGGAAATGgtaaggctgtagccttatagtcttatattgtaaatacgttctaagttgcatgcaatgcattatttgtatggtttcacatgaatttagttttctgatcctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA