Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttttttttttttttttggattgatttgaaattcttcattcgaataatgtttctgaattgagttggtatcttccttgtcttgtgtgaaccatttttggttgttgcttttgttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGATCCTGTTCCCGAAGAGGTTGGCATCTCTTTGATCAAACACGCATTCACCA

Basic information

species Glycine max
transcript GLYMA03G40680.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40680.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0030g02050.t01 (Vitis vinifera), 3'ss of exon 1
gttagttttttttttttttttggattgatttgaaattcttcattcgaataatgtttctgaattgagttggtatcttccttgtcttgtgtgaaccatttttggttgttgcttttgttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGATCCTGTTCCCGAAGAGGTTGGCATCTCTTTGATCAAACACGCATTCACCA
                   | |  | | | | ||    |||  |  | ||  | || |||  | |   |  |  ||   | |||  |       | |    |   |  ||||||  ||  | ||| || ||| | ||||||||||||||||| || | ||||| ||||||| |||||||| | ||||| |||||||| ||  | |||||  | |||||||  |
------------------atagtctaggtataaataaattctcttcattatggattttgagatcatgggagagattttatttctcattcagtttact----gaaatatcttttgccttaca-gGTCTCAAAGCTGGGATTTGGTTGTATGGGACTTACTGGAGAGTACAACCATCCTGTTTCAGAAGATGTTGGCATTTCAATCATCAAGTATGCATTCAGTA
















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|192325845|gb|FK018067.1|FK018067
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|192332295|gb|FK025960.1|FK025960
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|4396672|gb|AI495669.1|AI495669
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|298168820|gb|HO009750.1|HO009750
EST:     AAAAAATGGCAGATATTCCTCGGGTGAGGCTTGGAAGCCAAGGCCTGAAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|192334362|gb|FK025539.1|FK025539
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|4287645|gb|AI441219.1|AI441219
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|151410675|gb|EV280490.1|EV280490
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|192314627|gb|FK006385.1|FK006385
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|38192837|gb|CF922043.1|CF922043
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|298165604|gb|HO011653.1|HO011653
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGAAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|151411705|gb|EV281516.1|EV281516
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|13481916|gb|BG511259.1|BG511259
EST:     GCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: GCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|12773659|gb|BG238586.1|BG238586
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|192298309|gb|FG992099.1|FG992099
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAA                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|42722439|gb|CK768339.1|CK768339
EST:     AAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|192329671|gb|FK022937.1|FK022937
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|7146862|gb|AW508784.1|AW508784
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|192314626|gb|FK006384.1|FK006384
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|254315362|gb|GR825171.1|GR825171
EST:     AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
EST: gi|298181942|gb|HO026117.1|HO026117
EST:     GAAGAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGAAG                         GTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT
genomic: AAAAAATGGCAGATATTCCTCGGGTGAAGCTTGGAAGCCAAGGCCTGGAGgttagttttt ... gttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatcttccttgtcttgtgtgaaccatttttggttgttgcttttgttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGATCCTGTTCCCGAAGAGGTTGGCATCTCTTTGATCAAACACGCATTCACCA
                                        cttttgtttt  CT-rich tract
                                         ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttttttttttttttttggattgatttgaaattcttcattcgaataatgtttctgaattgagttggtatcttccttgtcttgtgtgaaccatttttggttgttgcttttgttttgtaagGTTTCCAAGTTAGGATTTGGTTGTATGGGCCTAAGTGGAGTGTACAACGATCCTGTTCCCGAAGAGGTTGGCATCTCTTTGATCAAACACGCATTCACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG