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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcttgtgataaacatagaccatcttgttttttccgtctagcttagtatcctaacggattactttacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA

Basic information

species Glycine max
transcript GLYMA13G22420.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 17
gtttgtcttgtgat--aaacatagaccatcttgttttttccgtctagcttagtatcctaacggattactttacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA
|||  ||||   ||  |||  |  ||   |   || |   | |     |  | ||  |   |    | |||        | |||||||||||  | || ||||||||||| || || ||||||| ||||||||| ||  || | ||||| ||||| || |  || ||||||||||||||||| |
gttaatcttcccatccaaaagtgaactgccaacttgtcaactttgttttctgaattttgttgc-ccattttgttcc---aacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA

upper sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 17
gtttgtcttgtgataaacatagaccatcttgttttttccgtctagcttagtatcct---aacggattactttacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA
||| | |||   ||   || ||  ||   |    |  || |  |  || |  |  |   || |   | | ||  ||   || |||||||| ||| | ||||||||| ||||||| || ||||||| ||||||||| ||  || ||||||||||||  || | ||| ||||| ||||| ||||| |
gttagcctttgcatccccagagtacaaaattcagtggcccttgaaatttgcgttttctgaatgccctccattttatcccga-cagCAAGCGGAAGCACAGATAAAGCGAAGAATGGGCATTGGAAGCCACATATCTGAGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCA

upper sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 17
------gtttg--tcttgtgataaacatagaccatc--ttgttttttccgtctagcttagtatcctaacggattactttacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA
       ||||  ||    | || ||| |   || |  |||    || | | |  || |    | |     |||  |||    | ||| |||||||| ||  | || |||||||||||||| || || || | ||||||||| ||  || ||||||||||||| || | | | ||||||||||||||||| |
gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcattttcctgaacggctttcatcatttttttttcatctga-cagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA

upper sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 16
lower sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 16
gtttgt--cttgtgataaacatagaccatcttgttttttccgtctagcttagtatcctaacggattactttacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA
||| ||  ||||||   || | |||  ||| |  | | ||         || || |  ||     || |          | |||||||| ||||| ||||||||||||||||| ||||| |||   |   ||||||| ||||| ||||| || || ||    |||||||| ||||| || || |
gttagttgcttgtggggaagaaaga--atcatcgtatctcta---gatgtaataactaaatttggtattggtgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA

upper sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 16
gtttgtcttgtgataaacatag--accatcttgttttttccgtctagcttagtatcctaacggattactt---tacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA----
         |||||  |||     |||  | | || | |     | | ||  |||  | ||  |  ||||   | |    ||| |||||||||||||| ||||||||||||||||| || ||||||| ||||||||| || ||| |||||||||||||  | | ||| ||||| |||||||||||||    
---------gtgattgacaccctcacctccattttctcttttctttgtttcttatttttactaac-acttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT

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|193325302|gb|FK289662.1|FK289662
EST:     ACCTGATATGGCAAATGAGATAAAG                         CAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCA
genomic: ACCTGATATGGCAAATGAGATAAAGgtttgtcttg ... ttgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttttttccgtctagcttagtatcctaacggattactttacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA
                         tcctaac  putative branch site (score: 1)
                                  attacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcttgtgataaacatagaccatcttgttttttccgtctagcttagtatcctaacggattactttacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT