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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGAGGCTGAGATTTCTCCTTCCACCTTGTATGCCATTGCCTGTGTGATGGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgcttgcctttatgtcccccccacaacttaaattgtttgtatttatgctaatttgtgaactttggtttgtgttgttgtcatcag

Basic information

species Glycine max
transcript GLYMA18G02210.4
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G02210.4 (Glycine max), 5'ss of exon 5
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 5'ss of exon 5
AATGAGGCTGAGATTTCTCCTTCCACCTTGTATGCCATTGCCTGTGTGATGGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgcttgcctttatgtcccccccacaacttaaattgtttgtatttatgctaatttgtgaactttggtttgtgttgttgtcatcag
 |||||||||||||||||||||| ||  | || |||||||| |||||  | || || |||||||| || |||||||| || || ||||||||||| || |||      ||    |  |      |   | |   | |||    |  | || |    | |  | |  ||| | || | || |         
GATGAGGCTGAGATTTCTCCTTCTACACTTTACGCCATTGCTTGTGTTCTTGAGAACGTTCCTTTTATCAATGGAAGTCCACAAAACACTTTTGTCCCTGgt----aactaaattaaactatatctagatagtattaatgaccttcaattttctatagtaatcacattttgcttatattatacag-----

upper sequence: GLYMA18G02210.4 (Glycine max), 5'ss of exon 5
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 5'ss of exon 5
AATGAGGCTGAGATTTCTCCTTCCACCTTGTATGCCATTGCCTGTGTGATGGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgcttgcctttatgtcccccccacaacttaaattgtttgtatttatgctaatt----tgtgaactttggtttgtgttgttgtcatcag-----------------
|||||| ||||||| ||||||||||||||||||||  | || ||||| |||||||||||||| || || ||||||||||| |||||||||||||| ||||||    |  |   ||  |  |  ||    | |  | ||   | || ||| ||  ||        ||  | | |   |  |||| ||||  |||                  
AATGAGCCTGAGATCTCTCCTTCCACCTTGTATGCTCTGGCTTGTGTCATGGAAAATGTTCCCTTTATCAATGGAAGCCCACAGAACACTTTTGTTCCAGgt----tcttaatctgaaattttccttttctatgtgaaggttatgaattcatcatagagggggcgtctaatctcactcatgtttttgttgtcaatctttgtatgtcttcag

upper sequence: GLYMA18G02210.4 (Glycine max), 5'ss of exon 5
lower sequence: EFJ37320 (Selaginella moellendorffii), 5'ss of exon 5
AATGAGGCTGAGATTTCTCCTTCCACCTTGTATGCCATTGCCTGTGTGATGGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgcttgcctttatgtcccccccacaacttaaattgtttgtatttatgctaatttgtgaactttggtttgtgttgttgtcatcag
 | ||| | || || ||||| |||||  | || ||| | || ||| |    ||   |||||||||||| || || ||||| |||||||||||||| ||||||    | ||| | ||| |   |||       ||    ||| |   |  | ||   ||    |     |||   |               
GACGAGCCCGAAATCTCTCCCTCCACTATTTACGCCTTGGCATGTATCCAAGAGGGTGTTCCTTTCATCAACGGGAGCCCCCAGAACACTTTTGTCCCAGgt---gtcctt-cgttttttctcccagtttttctcggtttgctaagaagtgtgtgtatgcacggtgcatggccag---------------

upper sequence: GLYMA18G02210.4 (Glycine max), 5'ss of exon 5
lower sequence: EFJ27629 (Selaginella moellendorffii), 5'ss of exon 5
AATGAGGCTGAGATTTCTCCTTCCACCTTGTATGCCATTGCCTGTGTGATGGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgcttgcctttatgtcccccccacaacttaaattgtttgtatttatgctaatttgtgaactttggtttgtgttgttgtcatcag
 | ||| | || || ||||| |||||  | || ||| | || ||| |    ||   |||||||||||| || || ||||| |||||||||||||| ||||||    | ||| | ||| |   |||       ||    ||| |   |  | ||   ||    |     |||   |               
GACGAGCCCGAAATCTCTCCCTCCACTATTTACGCCTTGGCGTGTATCCAAGAGGGTGTTCCTTTCATCAACGGGAGCCCCCAGAACACTTTTGTCCCAGgt---gtcctt-cgttttttctcccagtttttctcggtttgctaagaagtgtgtgtatgcacggtgcatggccag---------------

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|6502144|gb|AW203517.1|AW203517
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|19453629|gb|BM955039.1|BM955039
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|11413502|gb|BF425513.1|BF425513
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|193324768|gb|FK288036.1|FK288036
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|193402716|gb|FK367178.1|FK367178
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|193401065|gb|FK365430.1|FK365430
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|4296509|gb|AI442485.1|AI442485
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACCTTTGTACCAG                         GGCTTGAT-GATCTTGCCATCGCGAGGAAC
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCT-GATTGATCTTGCCATCGCGAGGAAC
EST: gi|19270872|gb|BM887128.1|BM887128
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|120530142|gb|EH258276.1|EH258276
EST:     GGAAAATGTTCCTTTCATCAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|6454183|gb|AW184796.1|AW184796
EST:     TTTCATTAATGGAAGTCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: TTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|208072570|gb|GD869830.1|GD869830
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|193356088|gb|FK322689.1|FK322689
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|207781450|gb|GD754001.1|GD754001
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|207834410|gb|GD806311.1|GD806311
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|13790045|gb|BG652636.1|BG652636
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
EST: gi|193424429|gb|FK391230.1|FK391230
EST:     GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAG                         GGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT
genomic: GGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgct ... ttgtcatcagGGCTGATTGATCTTGCCATCGCGAGGAACACTTTGATTGGTGGAGATGACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGAGGCTGAGATTTCTCCTTCCACCTTGTATGCCATTGCCTGTGTGATGGAAAATGTTCCTTTCATTAATGGAAGCCCTCAGAACACTTTTGTACCAGgttggatgcttgcctttatgtcccccccacaacttaaattgtttgtatttatgctaatttgtgaactttggtttgtgttgttgtcatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG