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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttaggtggaaaagattaatcttcctatccgtaaattacctatgtagctactaatgtcatttttctactcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG

Basic information

species Glycine max
transcript GLYMA05G01270.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 4
------------gtaagt-tttaggtg-----gaaaagattaatcttcctatccgtaaattacctatgtagctactaatgtcatttttctactcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG
            | |||   ||| ||      ||| ||  | || ||  | |   |  |||   | |     | ||||  |  |  || ||   |    ||||||||| ||||| || || || || |||||| |||||||||||||||| || |||||||||||||||||||||||||| || ||||||
tgctacttgtgtggaagcacttatgtaccttagaatagcatgatattgttgtatctccatttgttttact-ttcctaacattttccttttatcatgtacagTTTATGCTGATGGGAGCATATGCTTAGATATACTACAAAACCAGTGGAGCCCCATATATGATGTAGCTGCTATACTCACATCCATCCAG

upper sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110983_T02 (Zea mays), 3'ss of exon 3
gtaagttttaggtggaaaagatta--atcttcctatccgtaaattacctatgtagctactaatgtcatttttctactcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG
     | |||  |  |  |   ||  ||||||  || |       || ||| |   |     || |||||||||  | |  | ||||||||| |||||||| || || || |||||  | || || ||||||||||| ||||||||||||||||| |||||||| || ||||||
-----tcttaactatatgatggtactatcttctaatgc-----ccacttatatgtgtcaccctgacatttttctcatat--gcagtttatgctgatggaagcatatgcttagATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG

upper sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 2
--------------------gtaagttttaggtggaaaagattaatcttcctatccgtaaattacctatgtagctactaatgtcatttttctactcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG
                      || | |       | | |||    ||  || ||        || ||| |   |     || |||||||||  | |  | ||||||||| |||||||| || || || |||||  | || || ||||||||||| ||||||||||||||||| |||||||| || ||||||
ctcctctggcttattctgatacaactctcttaactatatgatggtactatct-tctaatgcccacttatatgtgtcaccctgacatttttctcatat--gcagTTTATGCTGATGGAAGCATATGCTTAGATATCCTGCAGAATCAGTGGAGTCCGATATATGATGTAGCTGCGATACTCACGTCAATCCAG

upper sequence: GLYMA05G01270.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttttaggtg-gaaaagattaatcttcctatccgtaaattacctatgtagctactaatgtcatttttctac------tcttgga------agTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG
|||||||  |  |  |     |||| | |  ||    || || ||  | | ||||| |   | || |  ||||||      | ||| |      ||| ||||| ||||||||||||||| | |||||  ||||||| |||||||||||||||||||||||||| |||||||| || ||||| |||
gtaagttggaactatgttgcaattagtatcacttcatgttaaatatttctttagctgc-ggtttcttacttctaccttttattttgaattggccagTCTATGCAGATGGAAGTATTTGTCTCGATATTCTACAAAATCAGTGGAGTCCTATATATGATGTAGCAGCTATACTTACGTCTATTCAG

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|192302663|gb|FG994901.1|FG994901
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|151408894|gb|EV278702.1|EV278702
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|15204594|gb|BI427362.1|BI427362
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|120530431|gb|EH258564.1|EH258564
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|21887693|gb|BQ740906.1|BQ740906
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|151398226|gb|EV268104.1|EV268104
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|208204410|gb|GE007817.1|GE007817
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|26047615|gb|CA784343.1|CA784343
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|31460020|gb|CD402048.1|CD402048
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|192299657|gb|FG990010.1|FG990010
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|192326016|gb|FK016198.1|FK016198
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|27427583|gb|CA939103.1|CA939103
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|10235637|gb|BE804525.1|BE804525
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|254349242|gb|GR860040.1|GR860040
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|4397477|gb|AI496474.1|AI496474
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATTCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTT
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|151396142|gb|EV266019.1|EV266019
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|7691194|gb|AW759326.1|AW759326
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
EST: gi|19054147|gb|BM732814.1|BM732814
EST:     AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACA                         TTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC
genomic: AAACAAGCCACCAACTGTACGATTTGTCTCTCGAATGTTTCATCCAAACAgtaagtttta ... ctcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctatccgtaaattacctatgtagctactaatgtcatttttctactcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG
                          tactaat  putative branch site (score: 1)
                                  tcatttttctactctt  CT-rich tract
                                    atttttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttaggtggaaaagattaatcttcctatccgtaaattacctatgtagctactaatgtcatttttctactcttggaagTTTATGCGGATGGAAGTATTTGTTTGGATATATTACAAAACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT