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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagatgttcacttttacatttgttatttcattttcatttatgaatcttcttgcttattgatcaactcactattactattgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGCATTCTTTAAAGGTTTCCTTGGAGGACGTCTATAACGGCACAACAAAGAA

Basic information

species Glycine max
transcript GLYMA07G14540.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G14540.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 3
gtga--gagatgttcacttttacatttgttatttcattttcatttatgaatcttcttgctt---attgatcaactcactatt--actattgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGCATTCTTTAAAGGTTTCCTTGGAGGACGTCTATAACGGCACAACAAAGAA---
|| |   | || |    |  |    ||  ||| |    ||  || |||  ||   |||  |   | |  |  |||   ||||   |  ||     |||   |||||||| ||  ||||  | ||||| |||| ||||||||||||||||||| || | ||||||||||| || ||  | || || || ||||| |||||   
gtaatcaaaatatcttgtggtgttgtttatatatatcgttgcttcatgcttccctttggattaaaatactacactggttatttatcggtttatggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT

upper sequence: GLYMA07G14540.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------gtgagagatgttcacttttacatttgt-----tatttcattttcatttatgaa----tcttc--ttgcttattgatcaactcactattactattgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGCATTCTTTAAAGGTTTCCTTGGAGGACGTCTATAACGGCACAACAAAGAA
                          |||    | || | |||| ||  |||     |||||| | |  |  | | ||    | |||  ||   |||| |   | || | | || | |  | |  ||||||||||||| ||  |||| ||||| ||||| |  ||||||||||| |||||| |||| |||||||| ||||||||| | ||||| |||||| |||||||
gtaagaggatgcttacttaaatttcttgatctttatttattttttcaaatgtgtacttatttcctgtctacctttaaagaaattttcaattatatatttactgattcccaagta-tctaattttgtagGTGGTGGTAGCTCAAGAGGAAGAAGGCAGAAACGAGGTGAAGATGTTGTGCATACTTTGAAGGTTTCTTTGGAGGACTTGTATAATGGCACATCAAAGAA
















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|33388612|gb|CA851819.1|CA851819
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|120491272|gb|EH219439.1|EH219439
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|18040211|gb|BM308505.1|BM308505
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|298172387|gb|HO019427.1|HO019427
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGCGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGATAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|254327121|gb|GR836730.1|GR836730
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|207760765|gb|GD734088.1|GD734088
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|254341868|gb|GR853005.1|GR853005
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|298173661|gb|HO016997.1|HO016997
EST:     TAATCCATTTGATATGTTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGATGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|192322850|gb|FK014781.1|FK014781
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGC-TT--TG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|207737525|gb|GD714127.1|GD714127
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|193647664|gb|FK588019.1|FK588019
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|163923429|gb|EH038356.1|EH038356
EST:     TTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTCTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|209702366|gb|BW656341.1|BW656341
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|11688808|gb|BF596484.1|BF596484
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
EST: gi|209709339|gb|BW678883.1|BW678883
EST:     TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTG                         GTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC
genomic: TAATCCATTTGATATATTTGAATCATTTTTTGGTGGAGCAAGCTTTGGTGgtgagagatg ... tgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttatgaatcttcttgcttattgatcaactcactattactattgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGCATTCTTTAAAGGTTTCCTTGGAGGACGTCTATAACGGCACAACAAAGAA
                             aactcac  putative branch site (score: 2)
                                            ttgtctctt  putative PPT
                                    tattactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagatgttcacttttacatttgttatttcattttcatttatgaatcttcttgcttattgatcaactcactattactattgtctcttagGTGGTGGTAGTTCCCGAGGTAGAAGACAGAAGCATGGTGAAGATGTGGTGCATTCTTTAAAGGTTTCCTTGGAGGACGTCTATAACGGCACAACAAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA