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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgatatttatatagcattgacacctatggttaaaaggtcatatcttacatgccttcttcgcaatttctagttaaagcatgaactaatctttaatatttaatatgttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACAAG

Basic information

species Glycine max
transcript GLYMA08G21300.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g02940.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtgtgatatttatatagcattgacacctatggttaaaaggtcatatcttacatgccttcttcgcaatttctagttaaagcatgaactaatctttaatatt-taatatgttcata---cagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACAAG
                                        |  ||| | | | |  |       |    ||    |   | |     || |  | | |||| |  | || |  |  ||   ||||||||| |||||||||||| ||    |||||||||||||||||||| ||||||
-------------------------------------gtgagtgtcttgtttcatttattgcagttaatatcatcaaacatattgaaaatt--tttgtaatctcatcatgttgttgtattgcagGGGACACATTCCCTGTTGGGTGTGCTTTTGATGAGTCCATTGTTCATCACAAG
















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|192304442|gb|FG997856.1|FG997856
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
EST: gi|17022499|gb|BM093533.1|BM093533
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
EST: gi|192310996|gb|FK001605.1|FK001605
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCC
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCC
EST: gi|58015895|gb|CX702637.1|CX702637
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
EST: gi|151397267|gb|EV267140.1|EV267140
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
EST: gi|14991768|gb|BI317441.1|BI317441
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
EST: gi|22540966|gb|BU090809.1|BU090809
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTACTCAATGGGCTGTAGTAG                         GGGACATATTCCCTG
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTG
EST: gi|14991788|gb|BI317461.1|BI317461
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
EST: gi|17023853|gb|BM094887.1|BM094887
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
EST: gi|151396455|gb|EV266332.1|EV266332
EST:     GTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGG-CTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
EST: gi|163921518|gb|EH039303.1|EH039303
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
EST: gi|58016178|gb|CX702920.1|CX702920
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
EST: gi|192295399|gb|FG987013.1|FG987013
EST:     GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAG                         GGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA
genomic: GGTGCTGAATTTGCCTAGTTTTGGAGGACTTCCTCAATGGGCTGTAGTAGgtatgtgtga ... gttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcaatttctagttaaagcatgaactaatctttaatatttaatatgttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACAAG
                      aactaatctttaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtgatatttatatagcattgacacctatggttaaaaggtcatatcttacatgccttcttcgcaatttctagttaaagcatgaactaatctttaatatttaatatgttcatacagGGGACATATTCCCTGTTGGTTGCAGATTTGATGAGTCCATTGTTCACCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT