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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttagtatagcatagtgaaattttgtttaatacaccgaagcatttaatatttgatgtgaatgtgatgatatgctaaacgtgttttgttacgtgaatagGTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATGCAACTTGTCAGGAATATAACCACCAATCCTGAAGTCAG

Basic information

species Glycine max
transcript GLYMA18G01340.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01340.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0010g02450.t01 (Vitis vinifera), 3'ss of exon 1
tgcttagtatagcatagtgaaattttgtttaatacaccgaagcatttaatatttgatgtgaatgtgatgatatgctaaacgtgttttgttacgt---gaatagGTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATGCAACTTGTCAGGAATATAACCACCAATCCTGAAGTCAG
   |||  | |      | |     | || | |  | |  |  ||  |   | | |||| | |   || || || |   |   |||| || |     | |||||| || || || || || |||||||||||||||||||| || ||||| ||||| ||||| || |||||   |||||| |||||||| ||
-ttttaaaaaatttcttttatgacattttaacttgatcctataatggagactgtcatgttattt--attatttgttttgcccttttttttcccaatgggatagGTGTATCCTCTCTTTGCAGCAGTTGGTGTGGCTGTTGGCATTTGCGGAATGCAGCTTGTTAGAAATATCTGCACCAACCCTGAAGTGAG
















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|19268928|gb|BM885184.1|BM885184
EST:     TCTCTTCTCAACATGGCCGCCAACAGATGGTTAAAACCTGAG                         GTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
genomic: TCTCTTCTCAACATGGCCGCCAACAGATGGTTAAAACCTGAGgtacttaatt ... acgtgaatagGTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
EST: gi|16346721|gb|BI972316.1|BI972316
EST:     TTCCTGCCTCTCTTCTCAACATGGCCGCCAACAGATGGTTAAAACCTGAG                         GTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
genomic: TTCCTGCCTCTCTTCTCAACATGGCCGCCAACAGATGGTTAAAACCTGAGgtacttaatt ... acgtgaatagGTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
EST: gi|31461386|gb|CD403414.1|CD403414
EST:     TTCCTGCCTCTCTTCTCAACATGGCCGCCAACAGATGGTTAAAACCTGAG                         GTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
genomic: TTCCTGCCTCTCTTCTCAACATGGCCGCCAACAGATGGTTAAAACCTGAGgtacttaatt ... acgtgaatagGTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
EST: gi|17153352|gb|BM143285.1|BM143285
EST:     CCTGCCTCTCTTCTCAACATGGCCGCCAACAGATGGTTAAAACCTGAG                         GTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
genomic: CCTGCCTCTCTTCTCAACATGGCCGCCAACAGATGGTTAAAACCTGAGgtacttaatt ... acgtgaatagGTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
EST: gi|23055646|gb|BU577680.1|BU577680
EST:     CGCCAACAGATGGTTAAAACCTGAG                         GTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
genomic: CGCCAACAGATGGTTAAAACCTGAGgtacttaatt ... acgtgaatagGTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
EST: gi|13562964|gb|BG551184.1|BG551184
EST:     TTCCTGCCTCTCTTCTCAACATGGCCGCCAACAGATGGTTAAAACCTGAG                         GTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG
genomic: TTCCTGCCTCTCTTCTCAACATGGCCGCCAACAGATGGTTAAAACCTGAGgtacttaatt ... acgtgaatagGTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatatttgatgtgaatgtgatgatatgctaaacgtgttttgttacgtgaatagGTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATGCAACTTGTCAGGAATATAACCACCAATCCTGAAGTCAG
                           tgctaaa  putative branch site (score: 2)
                                      ttttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttagtatagcatagtgaaattttgtttaatacaccgaagcatttaatatttgatgtgaatgtgatgatatgctaaacgtgttttgttacgtgaatagGTATACCCACTGTTCGCTGCAGTTGGTGTGGCTGTTGGGATCTGCGGTATGCAACTTGTCAGGAATATAACCACCAATCCTGAAGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG