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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAGAGGATTGCTCAACAAGCTCGTCTCTCGCTCCCTCTCGGTCGCCGGAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctctctctctctctctcaccgttatggatattattacgattcacaaatcaattccaattcgctatatactcctctcgctgaatctggatattat...

Basic information

species Glycine max
transcript GLYMA10G04480.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 1
GGTGAGAGGATTGCTCAACAAGCTCGTCTCTCGCTCCCTCTCGGTCGCCGGAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgt-ctctctctctctctctctctcaccgttatggatattattacgattcacaaatcaattccaattcgctatatactcctctcgctgaatctggatattat---------------------------------------
|||  | |||| ||||   ||||| | ||| ||| ||||||| |||||||| |||||||||||| | || |||||||||||||||||||||||||||||||| ||||  |   | |   | |           |||      || ||   |   || |||       | | | |  |    ||   || |  ||    |                                         
GGTTCGCGGATCGCTCGGGAAGCTGGCCTCGCGCGCCCTCTCCGTCGCCGGGAAATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgctcttgcaaccccctccaccagatcccgcagattcccgcaccatattccgttcgatttttgcgggtttttttttggagtcttcgatttaggggcctgggctaacgcgctagggttcgtggatgtgtgggtatcgcag

upper sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G094614_T01 (Zea mays), 5'ss of exon 1
GGTGAGAGGATTGCTCAACAAGCTCGTCTCTCGCTCCCTCTCGGTCGCCGGAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctctctctctctctctcaccgt-tatggatattattacgattcacaaatcaattccaattcgctatatactcctctcgctgaatctggatattat-------------------
|||  | |||| ||||  |||||| |  || ||| ||||||| |||||||| | |||||||||| | || ||||||||||||||||||||||||||||||||  ||  | ||| |    |  |||  |        |||| ||         | | | |     |    |  |  ||      | || ||  || | || |                   
GGTTCGCGGATCGCTCGGCAAGCTTGCATCGCGCGCCCTCTCCGTCGCCGGGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcctagcgctcccagattggcactttgccctcccattagtattgcgtgggatttattcgtgctattttggaggctaggactgatggattagggt-ttgtggattgtttgggtctgcag

upper sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G041429_T01 (Zea mays), 5'ss of exon 1
GGTGAGAGGATTGCTCAACAAGCTCGTCTCTCGCTCCCTCTCGGTCGCCGGAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctctctctctctctctcaccgt-tatggatattattacgattcaca---aatcaattc-caattcgctatatactcctctcgctgaatctggatattat-------------------
|||  | |||| ||||  |||||| |  || ||| ||||||| |||||||| | |||||||||| | || ||||||||||||||||||||||||||||||||  |   | ||| |    |  |||  |        ||| | | |  |  |     ||  ||||    |    |  |  ||      | || ||  || | || |                   
GGTTCGCGGATCGCTCGGCAAGCTTGCATCGCGCGCCCTCTCCGTCGCCGGGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcgctcccagattggcactttgccctcccattttcaagtattgcgtgggatttattcgtgctattttggaggctgggactgatggattagggt-ttgtggattgtttgggtctgtag

upper sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G064695_T04 (Zea mays), 5'ss of exon 2
GGTGAGAGGATTGCTCAACAAGCTCGTCTCTCGCTCCCTCTCGGTCGCCGGAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctctctctctctctctcaccgt-tatggatattattacgattcac---aaatcaattc-caattcgctatatactcctctcgctgaatctggatattat-------------------
                                                 || | |||||||||| | || ||||||||||||||||||||||||||||||||  |   | ||| |    |  |||  |        ||| | | |  |  |     ||  ||||    |    |  |  ||      | || ||  || | || |                   
-------------------------------------------------GGGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcgctcccagattggcactttgccctcccattttcaagtattgcgtgggatttattcgtgctattttggaggctgggactgatggattagggt-ttgtcgattgtttgggtctgcag

upper sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G064695_T03 (Zea mays), 5'ss of exon 1
GGTGAGAGGATTGCTCAACAAGCTCGTCTCTCGCTCCCTCTCGGTCGCC-GGAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctctctctctctctctcaccgt-tatggatattattacgattcaca---aatcaattc-caattcgctatatactcctctcgctgaatctggatattat-------------------
 ||  | |||| ||||  |||||| |  || ||| ||||||| |||||| || | |||||||||| | || ||||||||||||||||||||||||||||||||  |   | ||| |    |  |||  |        ||| | | |  |  |     ||  ||||    |    |  |  ||      | || ||  || | || |                   
-GTTCGCGGATCGCTCGGCAAGCTTGCATCGCGCGCCCTCTCCGTCGCCCGGGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcgctcccagattggcactttgccctcccattttcaagtattgcgtgggatttattcgtgctattttggaggctgggactgatggattagggt-ttgtcgattgtttgggtctgcag

upper sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 1
GGTGAGAGGATTGCTCAACAAGCTCGTCTCTCGCTCCCTCTCGGTCGCCGGAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctctctctctctctctcaccgttatggatattattacgattcacaaatcaattccaattcgctatatactcctctcgctgaatctggatattat--
||||||||||||| |||||||||| || |||||||| |||   ||||||||||||||||||||  | || |||||||| |||||||| |||||||| |||||| || | ||||||  ||| |  || |  | | |    ||   ||       ||  |     | |  | | |  | |  ||  |||      |||  |   
GGTGAGAGGATTGGTCAACAAGCTTGTATCTCGCTCTCTCAACGTCGCCGGAAAATGGCAGCAACAGCAGCTCCGCCGTCTCAACATTCACGAGTATCAGgtccct-tttctctccttctttttccatctttgttccatttttcatcttgtggtctctgatgttcccttttttgtttcgttca-tgaggtaacataagaaat

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|298172859|gb|HO019843.1|HO019843
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
EST: gi|298184950|gb|HO030163.1|HO030163
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
EST: gi|298176586|gb|HO023173.1|HO023173
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
EST: gi|61241640|gb|DN591031.1|DN591031
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
EST: gi|19347335|gb|BM892215.1|BM892215
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
EST: gi|4284430|gb|AI440780.1|AI440780
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
EST: gi|209712883|gb|BW679160.1|BW679160
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
EST: gi|192308759|gb|FG999784.1|FG999784
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
EST: gi|151397308|gb|EV267181.1|EV267181
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
EST: gi|4260145|gb|AI416641.1|AI416641
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
EST: gi|151409274|gb|EV279082.1|EV279082
EST:     GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAG                         GGTGCTGAATTGACGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT
genomic: GAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctct ... ataaacctagGGTGCTGAATTGATGAGCAAACACGGAGTCAACGTTCCGAGAGGCGTGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGAGAGGATTGCTCAACAAGCTCGTCTCTCGCTCCCTCTCGGTCGCCGGAAAATGGCAGCACAATCAACTCCGCCGCCTCAACATCCACGAGTACCAGgtctctctctctctctctctctcaccgttatggatattattacgattcacaaatcaattccaattcgctatatactcctctcgctgaatctggatattat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctctc