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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcagtcatgtttcatcttaatttttatttagtgaataggctgtacatcacttgttttgggagtctaattgaactgtagcttggggtaagttcaagcattggggtacccttggggatgaacaacatttacatgtattaatccattatcatgttattctaattttacttttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTTCGGTTAGTGCAGCGTACTAACATGAGCAAGAGGACGTTTGGAACTGATC

Basic information

species Glycine max
transcript GLYMA07G05230.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05230.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G53730.2 (Arabidopsis thaliana), 3'ss of exon 15
gtaatgtcagtcatgtttcatcttaatttttatttagtgaataggctgtacatcacttgttttgggagtctaattgaactgtagcttggggtaagttcaagcattggggtacccttggggatgaa-caacatttacatgtattaatccattatcatgttattctaattttacttttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTTCGGTTAGTGCAGCGTACTAACATGAGCAAGAGGACGTTTGGAACTGATC
                                                                                                          |   ||   |||  |  || | |   || ||  |   |     |  |    | ||| |   | |  |||     |||||||||||||| ||  ||||||| ||||| ||||| || || || || |||  |||||||||| |  |||||||||||||||| ||  | |||  |||||
----------------------------------------------------------------------------------------------------------gtaaactaatggtcacaaatcgagtcttgcaaattcaagaaagtcttttactgattttgggtcttgtttcttaacagCCGGAGCCGGAGTTTAGACCACCAATGTCTGAAGTTGTGCAGGCTCTAGTTGTGTTAGTGCAGAGAGCTAACATGAGCAAGAGAACTGTCGGAGTTGATC

upper sequence: GLYMA07G05230.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 15
gtaatgtcagtcatgtttcatcttaatttttatttagtgaataggctgtacatcacttgttttgggagtctaattgaactgtagcttggggtaagttcaagcattggggtacccttggggatgaacaacatttacatgtattaatccattatcatgttattctaattttacttttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTTCGGTTAGTGCAGCGTACTAACATGAGCAAGAGGACGTTTGGAACTGATC
                                                             |  || || || || || |  ||  ||  |   | |  | |||   | | |   ||  ||||              |||   |||  || ||   || |  || |||  | ||| |||||||| ||||| || ||||| ||||| |||||||||||||| ||||| ||||| ||| |||| |||||  | |||||||||||||| ||  || | |  || |
------------------------------------------------------------gtaaggtgtttagttaaagtaaagagtgcagatggattcatcatcctgtttcagctgctgatg--------------gtaaagatctgttctctgattttaatattttatcgttttgggcagCCTGAGCCAGAGTTCCGGCCACCAATGTCAGAAGTGGTGCAAGCACTGGTGCGGCTAGTCCAGCGGGCAAACATGAGCAAGAGAACCATTAGTAACGAAC
















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|6666117|gb|AW277576.1|AW277576
EST:     CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
EST: gi|7285544|gb|AW598031.1|AW598031
EST:     CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
EST: gi|22927841|gb|BU544980.1|BU544980
EST:     CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
EST: gi|193604920|gb|FK555002.1|FK555002
EST:     TCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: TCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
EST: gi|31456082|gb|CD398110.1|CD398110
EST:     CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
EST: gi|7029604|gb|AW459321.1|AW459321
EST:     CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCTGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
EST: gi|26047578|gb|CA784313.1|CA784313
EST:     CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
EST: gi|208318987|gb|GE112028.1|GE112028
EST:     CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCC
genomic: CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCC
EST: gi|214009532|gb|DB990118.1|DB990118
EST:     CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
EST: gi|298175534|gb|HO018245.1|HO018245
EST:     CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
EST: gi|209706450|gb|BW680737.1|BW680737
EST:     GTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: GTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
EST: gi|151400859|gb|EV270673.1|EV270673
EST:     CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAG                         CCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT
genomic: CTGTGAAGTCCCTTTCTCGATTTGCGGATGTTATTGCTCTGTGTGTTCAGgtaatgtcag ... tttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatttacatgtattaatccattatcatgttattctaattttacttttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTTCGGTTAGTGCAGCGTACTAACATGAGCAAGAGGACGTTTGGAACTGATC
                                ttctaat  putative branch site (score: 2)
                                      ttttactttt  CT-rich tract
                    attatcatgttattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtcagtcatgtttcatcttaatttttatttagtgaataggctgtacatcacttgttttgggagtctaattgaactgtagcttggggtaagttcaagcattggggtacccttggggatgaacaacatttacatgtattaatccattatcatgttattctaattttacttttggggcagCCGGAGCCGGAATTCCGACCACCTATGTCAGAAGTGGTTCAAGCGCTGGTTCGGTTAGTGCAGCGTACTAACATGAGCAAGAGGACGTTTGGAACTGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA