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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaagtattgaaggtgaattaaagaaactaaagtaccaagtaaaagttgaaaattcaatgattaccatcttatactggttcatgggttgcttgcctgcagGTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAGATGACTGATATCACTGATGAAGGTGTTTCAT

Basic information

species Glycine max
transcript GLYMA11G03230.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 2
tgaagtattgaaggtgaattaaagaaactaaagtaccaagtaaaagttgaaaattcaatgattac-catcttatactggttcatgggttgcttgcctgcagGTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAGATGACTGATATCACTGATGAAGGTGTTTCAT
    |||||   || ||||  | |||  |    | | |  |     |  ||  ||| ||  | |  ||  | | | ||  |||||  || |        ||||  |||| ||||| ||||||||||| |||||||||||    |||||||||||| | |||||||| || ||||| |||||||
----gtattcttggcgaatggaggaagatgttcttctagtt-----tcaaatgttccattttcatgcacataaaattgtgtcatgaatttc--------agGTTCTAATCATGGACAAACTTACTGTCAAGATAATGTCATTTTCATGCAAGATGGCAGATATCACAGAAGAAGGGGTTTCAT

upper sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 2
tgaagtattgaaggtgaattaaag-aaactaaagtaccaagtaaaagttgaaaattcaatgattaccatct-tatactggttcatgggttgcttgcctgca-----gGTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAGATGACTGATATCACTGATGAAGGTGTTTCAT
  | || ||    ||   | |  |   |||      |||  |||   ||      |  | | ||   | |  | |   || | |    || |||    | |     |||| |||| ||||| ||||||||||| |||||||||||  || | ||||| ||| ||||||||||  | ||||| |||||||
gtatgttttccttgtacttcactgtggactgg----ccagataatgtttttccgctttaaggttgatacccatttttcggctaaatatttcctttttcgtattttagGTACTAATCATGGACAAACTTACTGTCAAGATAATGTCGTACGCCTGCAAAATGGCTGATATCACACAAGAAGGAGTTTCAT
















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|19348894|gb|BM893426.1|BM893426
EST:     ATGAAATGCTGAGGTCATCAAAAACAGGGGATTCCAAATCAACTTGGAAG                         GTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAG
genomic: ATGAAATGCTGAGGTCATCAAAAACAGGGGATTCCAAATCAACTTGGAAGgtatatgatg ... ttgcctgcagGTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAG
EST: gi|254335297|gb|GR846794.1|GR846794
EST:     ATGAAATGCTGAGGTCATCAAAAACAGGGGATTCCAAATCAACTTGGAAG                         GTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAG
genomic: ATGAAATGCTGAGGTCATCAAAAACAGGGGATTCCAAATCAACTTGGAAGgtatatgatg ... ttgcctgcagGTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAG
EST: gi|209729055|gb|BW655059.1|BW655059
EST:     ATGAAATGCTGAGGTCATCAAAAACAGGGGATTCCAAATCAACTTGGAAG                         GTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAG
genomic: ATGAAATGCTGAGGTCATCAAAAACAGGGGATTCCAAATCAACTTGGAAGgtatatgatg ... ttgcctgcagGTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgaaaattcaatgattaccatcttatactggttcatgggttgcttgcctgcagGTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAGATGACTGATATCACTGATGAAGGTGTTTCAT
                                            cttgcct  CT-rich tract
     aaattcaatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaagtattgaaggtgaattaaagaaactaaagtaccaagtaaaagttgaaaattcaatgattaccatcttatactggttcatgggttgcttgcctgcagGTATTAATAATGGATAAACTTACTGTGAAGATAATGTCTCACTCATGCAAGATGACTGATATCACTGATGAAGGTGTTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - -ccaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgggttg