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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatgggtgatgatttgcgagctgatttttaacaaagccattctaatttgaacatggtgaaaagagtatattgttgacacaatattataatcagctctcatactggatagtaatatattttatcttaacttttatagGTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCAGGCCTTGCTTTGCAGCCG

Basic information

species Glycine max
transcript GLYMA05G37850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------gtgagatgggtgatgatttgcgagctgatttttaacaaagccat--tctaatt-tgaacatggtgaaaagagtatattgttgacacaatattataatcagctctcatactggatagtaat-atatttt--atcttaactttt--atagGTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCAGGCCTTGCTTTGCAGCCG
                                                 | | |    ||| |  |       || ||||| |  |    ||  |||| |  |     | |||||         || |  |   ||    |||||      ||  | |||| ||| || ||||||    | ||  ||| |  |||||| ||| ||||||| ||||||||| |||| ||||||| ||| |||||||  || |||||||||||||||
gtaagacaaatgctgcatttttggttaaacagtgatcaggtcattcatatcaaacccttgaaggctgatt--ttgttttttcatgattttatcttctattccttggttttgtgaattaccctgcttttaaattgaagtcaataatttatcttctgaatggaaagtgatgatatttctggtttttccttgttgatagGTTAATTTGGACTTCAGTTCTGAAACTGATATGATCAGGAAGTTTCGTGTTGGACTTGCTTTGCAGCCG
















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|19348212|gb|BM892744.1|BM892744
EST:     AAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTGCAG                         GTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCA
genomic: AAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTGCAGgtgagatggg ... acttttatagGTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCA
EST: gi|120496239|gb|EH224406.1|EH224406
EST:     AAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTGCAG                         GTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCCAGAAATTTCGTGCA
genomic: AAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTGCAGgtgagatggg ... acttttatagGTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCA
EST: gi|120493888|gb|EH222055.1|EH222055
EST:     AAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTGCAG                         GTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCA
genomic: AAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTGCAGgtgagatggg ... acttttatagGTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCA
EST: gi|9204205|gb|BE330429.1|BE330429
EST:     AAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTGCAG                         GTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCA
genomic: AAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTGCAGgtgagatggg ... acttttatagGTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattataatcagctctcatactggatagtaatatattttatcttaacttttatagGTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCAGGCCTTGCTTTGCAGCCG
                                        tcttaac  putative branch site (score: 2)
                                              cttttat  CT-rich tract
                        atagtaatatatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatgggtgatgatttgcgagctgatttttaacaaagccattctaatttgaacatggtgaaaagagtatattgttgacacaatattataatcagctctcatactggatagtaatatattttatcttaacttttatagGTCAATCTGGACTTTAGTTCTGAAGCTGACATGATCAAGAAATTTCGTGCAGGCCTTGCTTTGCAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA