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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaattcttatccactgaatgatgtattagtttagcctttcaaacagagtgacatatgatgctgtcatttttgtataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAAGACAAGAGGTATAAAAACCGGGAGCTGCAAACAATGCGCCTTCTTGACC

Basic information

species Glycine max
transcript GLYMA19G41420.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41420.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 4
gtatgaattcttatccactgaatgatgtattagtt-tagcctttcaaacagagtgacatatgatgctgtcatttt---------tgtataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAAGACAAGAGGTATAAAAACCGGGAGCTGCAAACAATGCGCCTTCTTGACC
||| |||| | |||   ||  | ||| |    ||| |   ||| || | |||   |  | | |||||||||||||         |||    |   |||| |||||||| ||||| ||||||||||||||||| || || ||||||||||||||||| ||||| ||||| || || ||||| ||||| ||||||||||
gtaagaatccatat---ctttacgatatgcctgttattttcttccacaaagaacaatttttcatgctgtcattttctggttttctgtgccttatcagGCAAAATGCTTAGAGACCGGTGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAACTTCAAACTATGCGTCTTCTTGACC

upper sequence: GLYMA19G41420.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 4
gtatgaattcttatccactgaatgatgtattagtttagcctttcaaacagagtgacatatgatgctgtcatttttgtat----aattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAAGACAAGAGGTATAAAAACCGGGAGCTGCAAACAATGCGCCTTCTTGACC
                       |   |  ||||  |  |  |  |||| |   |    | ||  | || | ||| | |     | || |||| || |||||||| || || ||||| |||||||||||||| || || ||||||||| |||| || ||||| ||||| || | ||||||||| || ||||
-----------------------gtattgctagtccaaacagtgcaacaaaagcaggctttatcgtttcttctttctctttgggaatgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGGTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

upper sequence: GLYMA19G41420.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 3
gtatgaattcttatccactgaatgatgtattagtttagcctttcaaacagagtgacatatgatgctgtcatttttgtataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAAGACAAGAGGTATAAAAACCGGGAGCTGCAAACAATGCGCCTTCTTGACC
                   |  ||     |   ||||  | |||    ||  | || | |  | ||||     ||     | |  |||| || ||| | || || || || || ||||| ||||| || ||  | || |||||||| || ||||||||||||||||||| |||||||||||||||||
-------------------gtgtgcaaactcgctttaatcattc---taggctaacgtttcttcctgttgggcttc----acttcagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCCATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

upper sequence: GLYMA19G41420.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 3
gtatgaattcttatccactgaatgatgtattagtttagcctttcaaacagagtgacatatgatgctgtcatttttgtataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAAGACAAGAGGTATAAAAACCGGGAGCTGCAAACAATGCGCCTTCTTGACC
                   |  ||     |   ||||  | |||    ||  | || | |  | ||||     ||     | | ||||| || ||| | || || || || || ||||||||||| || ||  | || |||||||| || ||||||||||||||||||| |||||||||||||||||
-------------------gtgtgcaaactcgctttaatcattc---taggctaacgtttcttcctgttgggcttc----actttagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCTATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

upper sequence: GLYMA19G41420.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 4
gtatgaattcttatccactgaatgatgtattagtttagcctttcaaacagagtgacatatgatgctgtcatttttgtataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAAGACAAGAGGTATAAAAACCGGGAGCTGCAAACAATGCGCCTTCTTGACC
                | ||   |    |  |||  | |     || |||  |   ||  | | ||    | | | |   | || |||| || |||||||| || || ||||| |||||||||||||| || || ||||||||| | || || ||||| ||||| || | ||||||||| || ||||
--------------gtattgctagtccaaacagtgcaaca---aaagcaggcttttat-cgtttcttctttctctttgggaatgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGCTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

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|213616919|gb|DB959231.1|DB959231
EST:     ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAG                         GCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
genomic: ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAGgtatgaattc ... ataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
EST: gi|13252730|gb|BG363633.1|BG363633
EST:     ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAT                         GCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
genomic: ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAGgtatgaattc ... ataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
EST: gi|15286620|gb|BI470511.1|BI470511
EST:     ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAG                         GCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
genomic: ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAGgtatgaattc ... ataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
EST: gi|254328746|gb|GR833118.1|GR833118
EST:     ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAG                         GCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
genomic: ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAGgtatgaattc ... ataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
EST: gi|209725616|gb|BW663105.1|BW663105
EST:     ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAG                         GCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
genomic: ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAGgtatgaattc ... ataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
EST: gi|6913877|gb|AW395407.1|AW395407
EST:     ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAG                         GCTAAATGCTTGGAGACTGGTGAAACTGTGGC
genomic: ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAGgtatgaattc ... ataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGC
EST: gi|213591319|gb|DB973808.1|DB973808
EST:     ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAG                         GCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
genomic: ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAGgtatgaattc ... ataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
EST: gi|298165875|gb|HO008846.1|HO008846
EST:     ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAG                         GCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
genomic: ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAGgtatgaattc ... ataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
EST: gi|15814589|gb|BI786864.1|BI786864
EST:     ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAG                         GCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA
genomic: ATATGGCAGAGCGGATTGTTGGACATGGATCATTTGGGGTTGTCTTCCAGgtatgaattc ... ataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttagcctttcaaacagagtgacatatgatgctgtcatttttgtataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAAGACAAGAGGTATAAAAACCGGGAGCTGCAAACAATGCGCCTTCTTGACC
                                     atttttgtataattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaattcttatccactgaatgatgtattagtttagcctttcaaacagagtgacatatgatgctgtcatttttgtataattgtagGCTAAATGCTTGGAGACTGGTGAAACTGTGGCTATCAAAAAAGTTCTTCAAGACAAGAGGTATAAAAACCGGGAGCTGCAAACAATGCGCCTTCTTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC