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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttttcttttgtttttgtcttcctatgcatagatatatggatggtatgatttctgagtttgatgtgttttgtggtgattttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTCCGAGTTGACAAGGTCCTTCAACCCT

Basic information

species Glycine max
transcript GLYMA14G02500.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G55120.1 (Arabidopsis thaliana), 3'ss of exon 3
---gtctgttttcttttgtttttgtcttcctatgcatagatatatggatggtatgatttctgagtttgatgtgt--tttgtggtg---att--ttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTCCGAGTTGACAAGGTCCTTCAACCCT
    || | ||    |||||  | | | | |  ||   ||   ||  ||  | || ||       ||||||| |  ||  |||||   |||  |  |  ||||| || || ||  | || |||||| |||| ||||| ||||| ||||| || ||||||||||||||||| |||||||| |||||||| || |||||||| |
agtttcaggttcacattgttgatatttacttgagct--gaagaatcaattttctgtttcacattgttgatgtttggttgttggtgtgcattggtaataatagGTTATACCGGGGAAGTACGGTTTCATTGCGCAGCTGAATGAAGGTCGGCATCTCAAGAAGAGACCAACCGAGTTCCGTGTTGACAAAGTTCTTCAACCAT

upper sequence: GLYMA14G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G26850.1 (Arabidopsis thaliana), 3'ss of exon 3
------gtctgttttcttttgttt--ttgtcttcctatgcatagatatatggatggtatgatttctgagtttgatgtgttttgt------ggtgattt-------tgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTCCGAGTTGACAAGGTCCTTCAACCCT
      |||| | ||   ||||||     |||   ||||    | | | ||      | || | |    | || | |   ||||      | |  |||       |||| ||||| || || ||  | |||||||||||||| |||||||| |||||||||||| | |||||||| |||||||||||||| || || |||||  | ||  | |
gtaattgtctttcttaccttgtttgacaatctagttatgttgggttgtttgttgctgaggaatccgagatatgttttacattgttcttaagattgtttctcttgatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT

upper sequence: GLYMA14G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0090g01000.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------gtctgttttct--tttgtttttgtctt----cctatgcatagatatatggatggtat---gatttctgagtttgatgtgttttgt--ggtgattttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTCCGAGTTGACAAGGTCCTTCAACCCT
                           || | ||| ||  || |||      ||      |  |  |     | ||| ||  |    |  || || ||||       |||||  | | |||       |||||||||| ||||| ||||| ||| |||||||||| |||||||| || ||||| |||||||| || ||||||||||| || || || ||||| || ||||
gtcagatattgattctgttcatctttagtttctttcctagttcgttgacaaattgggttttgggtttttcattgtggctgccaactggggttgtgggtttctctcaatttgtttgttaattcctgaccagGTGATTCCGGGTGAGTATGGGTTCATTGCCCAGCTGAATGAGGGCCGCCACCTGAAGAAGAGGCCCACTGAGTTCCGTGTGGATAAAGTCCTCCAGCCCT

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|120494153|gb|EH222320.1|EH222320
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATGCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGCGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttc ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC
EST: gi|11413203|gb|BF425214.1|BF425214
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttc ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC
EST: gi|6071672|gb|AW101059.1|AW101059
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttc ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC
EST: gi|19452462|gb|BM953872.1|BM953872
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttc ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC
EST: gi|9205432|gb|BE331656.1|BE331656
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttc ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC
EST: gi|151406689|gb|EV276504.1|EV276504
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttc ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatggatggtatgatttctgagtttgatgtgttttgtggtgattttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTCCGAGTTGACAAGGTCCTTCAACCCT
                       gtttgat  putative branch site (score: 5)
                                            ttttgtt  putative PPT
           tatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttttcttttgtttttgtcttcctatgcatagatatatggatggtatgatttctgagtttgatgtgttttgtggtgattttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTCCGAGTTGACAAGGTCCTTCAACCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA