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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaattggttgttgttgttgttgttggtagtggaaaacacactattaaaggagcaggatctttggagattcttactttctaaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGT

Basic information

species Glycine max
transcript GLYMA19G04340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G04340.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g41140.1 (Oryza sativa), 3'ss of exon 3
attaattggttgttgttgttgttgttggtagtggaaaacacactattaaaggagcaggatctttggagattct--tactttctaaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGT
 || ||||           ||   |      ||       ||| || ||      |    | |  ||  || |  || ||  || | | | | |   |||||| || |||   |||||||| | |||| | |   | ||||| |||||||| |||||||| || ||||||||||||||||| ||||||||    || || ||
gttgattgaaaaaaaaaactgacatcaaatctgttgttagcaccatgaacaatttatctgcctaagattttgtactaattcttacattatatcta--tgcagATTATACTTCTGAGAATCCTAGGATAGTAATGCAGTGCTCACATCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAAGCATGCCCTGT

upper sequence: GLYMA19G04340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G468260_T02 (Zea mays), 3'ss of exon 2
attaattggttgttgttgttgttgttggtagtggaaaacacactattaaaggagcaggatc----tttggagattcttactttctaaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGT
    |  |   | ||||        ||    |   |      || || |      |  |||    | |    ||| |||  |  |||  |   |    ||||||| ||   |   |||||||| | |||| | |   | ||||| || ||||| |||||||| || ||||||||||||||||| ||||||||    || || ||
---gaacgaaaggtgttcaaaactatgagcattacattttttctgttgatactttataatcacattctcactattgttatatattaatgtaactaaa-ttgcagATTATGATTCTGAGAATCCTAGGATAGTAATGCAGTGCTCACACCATTTCCACCTTGGCTGTATTTATGAGTGGATGGAAAGAAGTGAGGCATGCCCTGT

upper sequence: GLYMA19G04340.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G38895.1 (Arabidopsis thaliana), 3'ss of exon 3
-attaattggttgttgttgttgttgttggtagtggaaaacacactattaaaggagcaggatctttggagattcttactttctaaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGT
 ||||     ||  |  | | |||   |    ||    |  |  |   |  | |  | | |  |    | ||| || ||  |    | |       |||||| ||||||   |||||||| |||||||| || || || ||||| ||||| |||||| | || |||||||| ||||||||||||||||| |  || || ||
cattaggccattaatagtatagtttacgtagatgaggcaatcgttgcgagtgcattaaggtaatattggtttcatagttctttg-ttttaacaatatgcagATTACACTTTGGAGAATCCGAAGATAATCACCAAGTGTTCTCACCATTTCCACCTTAGCTGTATTTATGAATGGATGGAGAGAAGTGAAACTTGCCCCGT

upper sequence: GLYMA19G04340.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02290.1 (Arabidopsis thaliana), 3'ss of exon 3
attaattggttgttgttgttgttgttggtagtggaaaacacactattaaaggagcaggatctttggagattcttactttctaaactgttt-ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGT
                              ||   ||  |  | ||| ||  ||     | ||||    |||    ||  ||   ||||  ||  |||||||||| ||   |||||| ||||||||  |||||||||| || || ||||| |||||| ||||||||||||||||||||||||||||||| |||||||||||
------------------------------gtaataataatcccattcaac-agtctcctttttgttccttcagtattcatatcttgttggttttttgcagAATATACATCAGAGAACCCAAAGATTGTGACAAAATGTTCACACCATTTCCACCTTAGTTGCATTTATGAGTGGATGGAGAGAAGTGAAAACTGTCCAGT

upper sequence: GLYMA19G04340.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G15790.2 (Arabidopsis thaliana), 3'ss of exon 3
--attaattggttgttgttgttgttgttggtagtggaa-aacacactattaaaggagcaggatctttggagattcttactttctaaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGT
  ||| |||  |  |  || || || ||  |  ||||  ||  || | | |||| |||    | |  |       ||| ||  |    ||||||     | ||||||||    |||||| || |||||  | ||||| || ||||| ||||| |||||  ||||||||||||| ||||||||||||||||| ||||| || ||
gtattcattt-tcatctttttttttctttttcttggatcaatgcatt-tcaaagaagcttagtatcaga------ttatttcgtg---tgtttt-----gtagAATACATATCAGAGAACCCGAAGATTGTTACAAAGTGTTCTCACCATTTCCACCTCAGTTGCATTTATGAATGGATGGAGAGAAGTGAAAACTGCCCTGT

upper sequence: GLYMA19G04340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0083g01000.t01 (Vitis vinifera), 3'ss of exon 3
attaattggttgttgttgttgttgttggtagtggaaaacacactattaaaggagcaggatctttgg---agattcttactt-tctaaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGT
   |  | ||  || ||   |||| || |  ||  ||    |||   | |  || | | | |  ||   ||||||| | || |  | |||  | ||   ||||||||| |||  ||| ||||| ||||||||||||||||||||||| ||||||||||||||||| || ||||| ||||||||||||||||| |  ||||||||
---atcttgtcattattag-gttgatgattctgttaactgtactcaaatattagaatgttttagggtatagattctgatttgttcatacttatcttttatgcagAATATACTCCAGAAAATCCCAAGATAATGACAAAATGCTCTCACCATTTTCACCTTGGTTGTATATATGAATGGATGGAGAGAAGTGAAACATGTCCAGT

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|192330620|gb|FK022275.1|FK022275
EST:     TGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAGgtagagatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|209724100|gb|BW654527.1|BW654527
EST:     ATGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: ATGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAGgtagagatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|7284555|gb|AW597143.1|AW597143
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAGgtagagatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|213594111|gb|DB981411.1|DB981411
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAGgtagagatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|213594611|gb|DB979475.1|DB979475
EST:     AAACTATGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAGgtagagatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
EST: gi|209715857|gb|BW674416.1|BW674416
EST:     TGTCTATGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAG                         AATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC
genomic: TGTCTATGCATCATCAGAGGAGGAGGATGTTTGTCCAACTTGTCTTGAAGgtagagatat ... ttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaggagcaggatctttggagattcttactttctaaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGT
                                ttctaaa  putative branch site (score: 2)
                                          tttttgctt  putative PPT
                               tttctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaattggttgttgttgttgttgttggtagtggaaaacacactattaaaggagcaggatctttggagattcttactttctaaactgtttttgcttgcagAATACACTAAAGAGAATCCAAAGATAATGACAAAATGCTCTCATCATTTTCACCTTGGTTGCATTTATGAGTGGATGGAGAGAAGTGACAACTGTCCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - gttgttg
- - - - - - - - - - - - - ggtagtg
- - - - - - - - - - - - - - - - - - aacacac