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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttattctagaatctagatttagttgttagattttgtttttgtagctcctccgtgaatgatgagaaaataagagttttgatgtgataatcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATGGACTGTCTTCTCTGACATAGAAAATAAAGGTTGCAGTAAAGAGGATCTA

Basic information

species Glycine max
transcript GLYMA10G32470.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
----tgcttatt-ctagaatctagatttagttgttagatt-ttgtttttgtagctcctccgtgaatgatgagaaaataagagttttgatgtgataatcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATGGACTGTCTTCTCTGACATAGAAAATAAAGGTTGCAGTAAAGAGGATCTA
    | || |||  | |  | | |||  |||| | |  || |  |  || ||         ||     ||  |   ||     |   || | ||     ||  ||||||||||||||| ||||| || || || ||||| ||| | || ||||||||||| |||||||||||| | || || | |||||||||   ||| ||||| 
ttactactgattgtttgtgtttggat--agttatcaacttgtcatgattatactaaggatatgtcctctgtaatttta----ctcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC

upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 7
tgcttattctagaatctagatttagt-tgttagatt---ttgtttttgtagctcctccgtgaatgatgagaaaataagagttttgatgtgataatcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATGGACTGTCTTCTCTGACATAGAAAATAAAGGTTGCAGTAAAGAGGATCTA
   | ||| || |   |     | || ||  | |     |||    || || |     |||   |||    ||||   | |       ||||    ||   |||||||||||| || || || || || ||||| || |||||||| || || |||||||| ||||||||||| ||||| ||||| || |||   |||||||| 
---tgattataaaccatgaggatggtgtgaaaaagaaaattgaaactgaagtttgat-gtggtagatattgaaattcaattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG

upper sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S140_59V6.2 (Physcomitrella patens), 3'ss of exon 7
tgcttattctagaatctagatttagttgttagattttgtttttgtagctcctccgtgaatgatgagaaaataagagttttg-atgtgataatcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATGGACTGTCTTCTCTGACATAGAAAATAAAGGTTGCAGTAAAGAGGATCTA
   |||   ||        | ||  ||||       | ||      | |  |    ||| | |  ||   | |   |   | ||||| |    |    |||||||||||| ||||| |||||||| || ||||||||| | || |||||||||||||| ||||| || || ||  |||||   ||||| |   | ||||| 
catttacaatatttgtcgtacttgtttgtgtcgcaattttggctaggattttataggaacgttttgagcttgaacttgaagtatgtggtggaat-gttcagGTGTGAAGCTTTTTCGACATACCCGCGCACATACGATCTGCTGCATGCATGGACTGTATTCTCAGATATTGAGGATAAAAACTGCAGAATTAAAGATCTT

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|8402835|gb|BE058469.1|BE058469
EST:     AGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTG                         GTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
genomic: AGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTGgtattgaagc ... tcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
EST: gi|16348530|gb|BI974125.1|BI974125
EST:     ACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTG                         GTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
genomic: ACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTGgtattgaagc ... tcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
EST: gi|14259513|gb|BG882421.1|BG882421
EST:     ACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTG                         GTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
genomic: ACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTGgtattgaagc ... tcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
EST: gi|207821165|gb|GD792232.1|GD792232
EST:     ACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTG                         GTGTGAAGCATATTCAACATACCCCCGGACTTATGATTTACTCCATGCATG
genomic: ACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTGgtattgaagc ... tcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
EST: gi|17021620|gb|BM092654.1|BM092654
EST:     ACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTG                         GTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
genomic: ACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTGgtattgaagc ... tcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
EST: gi|13479894|gb|BG509237.1|BG509237
EST:     ACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTG                         GTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
genomic: ACACTTAAGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTGgtattgaagc ... tcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
EST: gi|15203329|gb|BI426097.1|BI426097
EST:     AGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTG                         GTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG
genomic: AGCTCATATATGACAGAGGCCTTATAGGAACTACTCATGACTGgtattgaagc ... tcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctcctccgtgaatgatgagaaaataagagttttgatgtgataatcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATGGACTGTCTTCTCTGACATAGAAAATAAAGGTTGCAGTAAAGAGGATCTA
                               ttttgat  putative branch site (score: 4)
                     aaaataagagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttattctagaatctagatttagttgttagattttgtttttgtagctcctccgtgaatgatgagaaaataagagttttgatgtgataatcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATGGACTGTCTTCTCTGACATAGAAAATAAAGGTTGCAGTAAAGAGGATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
tgcttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtg