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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttgtttataatttcatttgattttgaaaaatgtttcttagacaacccttgagagagaaaggaagagatgagaaatgagtgattgatgatgtagcgtgataagaagagagaaaagataattgttggttgagtgtaagaaacttttgtacgtggattcatcatcaattagttaattatgctatgctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTCGCTGGTTCTGCTGCCTTTTTTCCCGATACTCTGAAGCAGAATGTTGATT

Basic information

species Glycine max
transcript GLYMA20G39400.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G39400.3 (Glycine max), 3'ss of exon 1
lower sequence: AT1G28140.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgttgtttataatttcatttgattttgaaaaatgtttcttagacaacccttgagagagaaaggaagagatgagaaatgagtgattgatgatgtagcgtgataagaagagagaaaagataattgttggttgagtgtaagaaacttttgtacgtggattcatcatcaattagttaattatgctatgctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTCGCTGGTTCTGCTGCCTTTTTTCCCG-ATACTCTGAAGCAGAATGTTGATT
                                  || ||||       |       ||     |   |  | | |  || ||   | |  | || |  |  |    | ||    | |  ||||  |   |      |      | | ||     | |   |||     | | | | ||   | | || |  ||||| |||||||||||||||||| | ||||| ||||||||||| ||||| |  |||  ||||||||||||||| || | | |||||     |        |  
----------------------------------gtctcttctcttctctccttacgattcctgcccaattcacacttgggttcctca--aagttgaatccttttgatagttttaggccaatttgttcatattctcatagtcatgtagtttagaggtagctcaagttgttgatgagtacctttttctctt-cagGTTATTTTGTACAGATCAGGACTAGTAACTGCTGCTGCATCTTTTGTAGCTGCTTCTTCTGCTGCCTTTTTACCAGGAGACTCTTGGTTAAGTGAAACAA-
















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|192316444|gb|FK006763.1|FK006763
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|298164949|gb|HO010946.1|HO010946
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|20075939|gb|BQ094722.1|BQ094722
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|298199151|gb|HO042514.1|HO042514
EST:     GTGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|192314495|gb|FK006337.1|FK006337
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|298198326|gb|HO039865.1|HO039865
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|208336628|gb|GE135956.1|GE135956
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|192314494|gb|FK006336.1|FK006336
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|193579825|gb|FK537756.1|FK537756
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCAT
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCAT
EST: gi|298167260|gb|HO010699.1|HO010699
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|298173956|gb|HO017292.1|HO017292
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|298168764|gb|HO009694.1|HO009694
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|209699464|gb|BW667650.1|BW667650
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|17519753|gb|BM188795.1|BM188795
EST:     ATGAGGTTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|15285717|gb|BI469608.1|BI469608
EST:     TTATTGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: TGA-GGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|298196387|gb|HO041130.1|HO041130
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|298166445|gb|HO009884.1|HO009884
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTCTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|20813455|gb|BQ297933.1|BQ297933
EST:     GGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: GGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|209701325|gb|BW655920.1|BW655920
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|120492033|gb|EH220200.1|EH220200
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|298194235|gb|HO040883.1|HO040883
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|192316445|gb|FK006764.1|FK006764
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|120532229|gb|EH260362.1|EH260362
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|120492075|gb|EH220242.1|EH220242
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|213596278|gb|DB961978.1|DB961978
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|120494591|gb|EH222758.1|EH222758
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
EST: gi|120534422|gb|EH262555.1|EH262555
EST:     ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAG                         GTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC
genomic: ATGAGGGTATTTATGGCCCCTGGACCATTGACGACTCCGATGTTCGAGAGgtgttgttta ... gctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacttttgtacgtggattcatcatcaattagttaattatgctatgctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTCGCTGGTTCTGCTGCCTTTTTTCCCGATACTCTGAAGCAGAATGTTGATT
                              agttaat  putative branch site (score: 4)
                       atcaattagttaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttgtttataatttcatttgattttgaaaaatgtttcttagacaacccttgagagagaaaggaagagatgagaaatgagtgattgatgatgtagcgtgataagaagagagaaaagataattgttggttgagtgtaagaaacttttgtacgtggattcatcatcaattagttaattatgctatgctatggcagGTAATTTTGTACAGATCAGGATTGGTAACAGCTGCTGCATCATTTGTGGTCGCTGGTTCTGCTGCCTTTTTTCCCGATACTCTGAAGCAGAATGTTGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC