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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGTGAACCTAATGCTCGCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaaactctttcttggtcatactggtgctttggcagtaaattatttgtactgacaatcttaaaggctaggaataaaattgattctattttt...

Basic information

species Glycine max
transcript GLYMA06G06850.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G06850.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 5'ss of exon 11
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGTGAACCTAATGCTCGCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaaactctttcttggtcatactggtgctttggcagtaaattatttgtactgacaatcttaaaggctaggaataaaattgattctattttt------------
||| |||||||||||||||||||||||||| || || || || ||||| ||||||||||| || ||||||||||| || ||||| ||||||||||| |||||||||   | | |       |              |||  |   |   | ||   |    | |    ||    |   |      |||| | ||   |||            
TGATGCATGTGCACATCCTTTCTTTGATGAGCTGCGAGAGCCGAATGCACGCTTGCCAAACGGACGTCCATTTCCACCACTATTCAACTTCAAACACGAAgtaagtgaatcagatgaaacataatctgctacacaacttcagatcttggt-atccatgagaaaatgtgtactctccttggtgctcattggtgctgccttttggtctctacag

upper sequence: GLYMA06G06850.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGTGAACCTAATGCTCGCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaaactctttcttggtcatactggtgctttggcagtaaattatttgtactgaca-atcttaaaggctaggaataaaattgattctattttt---
||| |||||||||||| | ||||||||||| || || || || ||||| ||| ||||||||||||||||||| || ||||| || |||||||| || |||||||||     | |   |||     ||| || |  |||||     |     |||| || | ||   || |  | |||    | |   |   ||||  | |    
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgagaacattt-----tcaaacagtcgcttt--ttatggtacatttatatttacctgtcatggatgcttatca-atgctcatttctggtatgcag

upper sequence: GLYMA06G06850.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 5'ss of exon 11
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGTGAACCTAATGCTCGCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaaactctttcttgg-----tcatactg-gtgctttggcagtaaattatttgtactgacaatcttaaaggctaggaataaaattgattctattttt
 ||||||||||||||||||||||||||||| || || ||||| ||||| ||| ||||||||||||||||||| || ||||| || || || || |||||||||||   ||  |  |  || ||       | || ||   |  |||   |   ||||  ||||     ||  || ||    |  |   | ||||  ||| ||    
AGAAGCATGTGCACATCCTTTCTTTGATGAGCTCCGAGAACCCAATGCCCGCCTGCCAAATGGTCGTCCATTACCACCTCTCTTCAATTTTAAGCAGGAAgtaagggtttttattttatttttatattttttattctatataatttctaaactaatttcttgtctc--cagcctgaacatgtctgtccataatttcttc-atg---

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|10236817|gb|BE805705.1|BE805705
EST:     GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAA                         TTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
genomic: GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgtttacagTTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
EST: gi|6482526|gb|AW201783.1|AW201783
EST:     GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAA                         TTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
genomic: GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgtttacagTTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
EST: gi|26060057|gb|CA802971.1|CA802971
EST:     TTTCCCCCTCTATTTACCTTCAAACAGGAA                         TTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
genomic: TTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgtttacagTTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
EST: gi|4396345|gb|AI495342.1|AI495342
EST:     GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAA                         TTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
genomic: GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgtttacagTTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
EST: gi|17022657|gb|BM093691.1|BM093691
EST:     GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAA                         TTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
genomic: GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgtttacagTTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
EST: gi|254320416|gb|GR826865.1|GR826865
EST:     GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAA                         TTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
genomic: GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgtttacagTTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
EST: gi|7285804|gb|AW598291.1|AW598291
EST:     TTCAAACAGGAA                         TTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
genomic: TTCAAACAGGAAgtaagtcctt ... ctgtttacagTTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
EST: gi|7590646|gb|AW706394.1|AW706394
EST:     GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAA                         TTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
genomic: GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgtttacagTTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
EST: gi|10843146|gb|BF066460.1|BF066460
EST:     GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAA                         TTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG
genomic: GCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtcctt ... ctgtttacagTTATCTGGAGCATCTTCCGAGCTTGTTAATAAGTTGATACCTGACCATGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGTGAACCTAATGCTCGCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaaactctttcttggtcatactggtgctttggcagtaaattatttgtactgacaatcttaaaggctaggaataaaattgattctattttt

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