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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatatgatgttttcactcttcattcctttttattatcctccaatgtagtctatcgatgcatgtttaatatatgttgtatcatttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAA

Basic information

species Glycine max
transcript GLYMA04G39520.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 3
gtgagcatatgatgttttcactcttcattcctttttattatcctccaatgtagtct-atcgatgcatgtttaatatatgttgtatcatttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAA
||||| ||   |||  | | |   | ||| |||     ||   |  ||||   | | ||   || |   | | |  || | | ||||  || |||||||| || ||||| ||||||||  | |||||||| | ||||||||||||||| || || || ||||  || | ||| ||||||||||| ||||||||| 
gtgagaatc--atggctactcaaat-attgcttacctataagatttaatgccctttcatgtgtgtaatctcactg-atat-gcatcaactg-tagATATATGTGGAGATAGAGAGAGCAAGATTGATCAAAAGACTTGCAAAAATCAAAGAGGAGCAGGGACAGATTGATGAGGCTGCTGATTTAATGCAAGAAG

upper sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 3
--gtgagcatatgatgttttcactcttcattcctttttattatcctccaatgtagtctatcgatgcatgtttaatatatgttgtatcatttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAA
  | ||   |||||   |     | |  |||| || | || |  || ||   |  ||| |   |   ||||||  ||    | |  ||| |  |||||||| ||||| || ||||| || ||  | | |||||||||||| || || ||||||||||| || |  |||||||||||||| ||| | ||||||||| 
gtgcgaaactatgaaactgatggtgt--attctttataataa--cttcatcat--tctgt--gtaattgtttaccattgcattttacatgta-tagATATATGTTGAAATCGAGAGGGCACGTCTCACCAAGAAACTTGCTAAGATTAAGGAAGAACAGGGTCAGATAGCTGAAGCTGCAGATCTTATGCAAGAAG

upper sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 3'ss of exon 3
------gtgagcatatgatgttttcactcttcattcctttttattatcctccaatgtagtctatcgatgcatgttt-----------aatatatgt-tgt-atcatttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAA
       | ||  |  | | || |   | ||  |    || ||||  | |  |   |  ||  ||  |||| ||||           ||||| ||| ||| | ||| || |||||||| || || || ||||||||||| |||| |||||  ||||| || || ||||||||||||||  | || ||||||||||| ||| | ||||||||| 
gtgcggattagagttggctattgttgttgttgttgtagttatatttgcttgaatcttgatcactccgtgcaagtttttttcttgatgaatatgtgtgtgtgagcatgtg-tagATATATGTCGAAATCGAGAGAGCTCGTTTGACCAAGATGCTTGCTAAGATTAAGGAAGAACAAGGTTTGATTGCTGAAGCTGCGGATCTCATGCAAGAAG

upper sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 3
gtgagcatatgatgttttcactcttcattcctttttattatcctccaatgtagtctatcgatgcatgtttaata------tatgt-tgtatcatttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAA
|| |  | || || | |  |   ||||     | ||||  |    ||||||  | | | | |    | ||  ||      ||| | || || |||   |||||||| ||||| || ||||| |||||| ||||||||||||| |||||||| |||||||| ||||| | ||||||||| || |||||||||||||||||||
gtcaatacat-atatctataagtttcagcttatattat-gttggacaatgtttttttttgttttgagctttttagttaattatatctgcattattatgtagATATATGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATAAAGGAAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAA

upper sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 3
gtgagcatatgatgttttcactcttcattccttt--ttattatcctccaatg----tagtctat-cgatgcat-gtttaatatatgttgtatcatttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAA
 || |  | |  | ||     | | | | | |    || | |  | |  |||    | ||   | | ||| || | || |  ||| | ||  |  | || |||||||||||||||| || |||||||| || |||||||| || || || ||||||||||||||||||   || || |||||||| ||||  ||||||||| 
ctgtgtgtgtatttttgcgggtgtgcgtgcatgcgcttgtaaaacacatatggtgatggttcgtacaatgtatagattgacgtat-tggtgacgat-gccagATATACGTTGAGATAGAAAGAGCTCGCTTAATCAAGAAGCTAGCGAAGATCAAGGAAGAACAAGGAAACATCGCCGAAGCTGCGGATTGCATGCAAGAAG

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|208233022|gb|GE032775.1|GE032775
EST:     AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
EST: gi|193674954|gb|FK616072.1|FK616072
EST:     AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
EST: gi|207815517|gb|GD788682.1|GD788682
EST:     AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
EST: gi|20812745|gb|BQ297231.1|BQ297231
EST:     AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
EST: gi|208080953|gb|GD873823.1|GD873823
EST:     AACTCGTATAGAACTCATCAAAATCTTGAACAGTGGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: AACTCGTATAGAACTCATCAAAATCTTGAACAGT-GTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
EST: gi|20207825|gb|BQ133914.1|BQ133914
EST:     AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
EST: gi|15284713|gb|BI468604.1|BI468604
EST:     AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
EST: gi|193530760|gb|FK484523.1|FK484523
EST:     TGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: TGTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
EST: gi|192297411|gb|FG990689.1|FG990689
EST:     AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
EST: gi|7478560|gb|AW666314.1|AW666314
EST:     AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
EST: gi|11274759|gb|BF325094.1|BF325094
EST:     AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAG                         ATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC
genomic: AAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTGCAGGAAAGgtgagcatat ... catttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctccaatgtagtctatcgatgcatgtttaatatatgttgtatcatttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAA
                           gtttaat  putative branch site (score: 4)
                            tttaatatatgttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcatatgatgttttcactcttcattcctttttattatcctccaatgtagtctatcgatgcatgtttaatatatgttgtatcatttgctagATATACGTTGAGATTGAGAGAGCTCGGTTGATCAAGAAACTTGCAAAAATCAAGGAAGAACAAGGACTTATAGCTGAAGCTGCTGATTTGATGCAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA