Sequence
atgc intronic sequence ATGC exonic sequence...gatgaatcaaatcctttttctaatactcaatattttgagactaatattggaactaaatcctttatttaagagaatattatttttcttttctttcttctagGGGACACTTAATGATGGAAGAGTCATTGCTGTGAAACAACTATCTGTGGGATCCCATCAAGGAAAGAGCCAATTCATAACTGAGATTGCTACTATATCAG
Basic information
species | Glycine max |
transcript | GLYMA08G25600.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G25600.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv12s0055g00580.t01 (Vitis vinifera), 3'ss of exon 20
--------------gatgaatcaaatcctttttctaatactcaatattttgag-actaatattggaa----ctaaatc-------ctttatttaagagaatattatttttcttttctttcttctagGGGACACTTAATGATGGAAGAGTCATTGCTGTGAAACAACTATCTGTGGGATCCCATCAAGGAAAGAGCCAATTCATAACTGAGATTGCTACTATATCAG
|| | | || |||| | || | | | | ||| || || || ||| || |||| ||| ||| || || |||| | ||| | |||||||||||| |||||||||||| ||||||| || ||||||||||| ||| || |||||||||| || || |||| |||||||| || |||||||
gtaggtcattatcctatcgagcttatatatttttttatgattatgagtatgattacaaacatgggatttttctcaatcattcctttttttttttttttggtaataattttatattcaattcgttagGGGACACTTTCTGATGGAAGAGTTGTTGCTGTAAAGCAACTATCTGTATCATCACACCAAGGAAAGAATCAGTTTGTAACAGAGATTGCAACCATATCAG
upper sequence: GLYMA08G25600.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv12s0055g00590.t01 (Vitis vinifera), 3'ss of exon 20
---------------gatgaatcaaatcctttttctaatactcaatattttgag-actaatattggaactaaatcctttatttaagagaatattatttttc------ttttctttcttctagGGGACACTTAATGATGGAAGAGTCATTGCTGTGAAACAACTATCTGTGGGATCCCATCAAGGAAAGAGCCAATTCATAACTGAGATTGCTACTATATCAG
||| | ||||| | || | | ||| ||| || || || | | | || || | | || ||||| |||| | | |||||||||||| |||||||||||| ||||||| || ||||||||||| | |||||| |||||||||| || || || | |||||||| || |||||||
gtaggtcattatcctattgagcttatattttttttttatgattataattatgattacaaacatggtatttttctcattctccttttttttttttttttttgcaataattttatattcgttagGGGACACTTTCTGATGGAAGAGTTGTTGCTGTAAAGCAACTATCTGTAGCATCCCACCAAGGAAAGAAGCAGTTTGTAGCAGAGATTGCAACCATATCAG
upper sequence: GLYMA08G25600.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv12s0055g00590.t01 (Vitis vinifera), 3'ss of exon 45
---------------gatgaatcaaatcctttttctaatactcaatattttgagactaatattggaactaaatcctttatttaagagaatattatttttcttttctttcttctagGGGACACTTAATGATGGAAGAGTCATTGCTGTGAAACAACTATCTGTGGGATCCCATCAAGGAAAGAGCCAATTCATAACTGAGATTGCTACTATATCAG
| ||| | ||||| || | | | | || || || ||| | || | ||| | |||| | | | ||| | |||||||||||| |||||||||||| ||||||| || ||||||||||| ||| || |||||||||| || || |||| |||||| || |||||||
gtaggtcattatcctgttgagcttatatatttttttatgattatgagtatgattacaaacatgggatttttctcaatcattctttttttttttatatatatattcaattcgttagGGGACACTTTCTGATGGAAGAGTTGTTGCTGTAAAGCAACTATCTGTATCATCGCACCAAGGAAAGAATCAGTTTGTAACAGAGATTAAAACCATATCAG
upper sequence: GLYMA08G25600.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv12s0055g00610.t01 (Vitis vinifera), 3'ss of exon 2
gatgaatcaaatcctttttctaatactcaatattttgagactaatattggaacta--aatcctttatttaagagaatattatttttcttttctt------------tcttctagGGGACACTTAATGATGGAAGAGTCATTGCTGTGAAACAACTATCTGTGGGATCCCATCAAGGAAAGAGCCAATTCATAACTGAGATTGCTACTATATCAG
| ||| | | | | | | | |||| || || ||| | || || ||||| ||| || ||||| |||| | | ||||||||||| |||||||||||| ||||||| || ||||||||||| |||||| |||||||||| | || |||| |||||||| || |||||||
-gtaggtcat-tatcctattgagcagatatttttttatgattatgattatgattacgaacatggtatttttctcaatcttctttttttttttgtcataattttatattcgttagGGGACACTCTCTGATGGAAGAGTTGTTGCTGTAAAGCAACTATCTGTATCATCCCACCAAGGAAAGAATCCGTTTGTAACAGAGATTGCAACCATATCAGMapped 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|120491096|gb|EH219263.1|EH219263EST: TTAATCTTGAAAATAAGCTTGGAGAGGGAGGTTTTGGACCTGTTTATAAG GGGACACTTAATGATGGAAGAGTCATTGCTGTGAAACAACTATCTGTGGGA
genomic: TTAATCTTGAAAATAAGCTTGGAGAGGGAGGTTTTGGACCTGTTTATAAGgtaatattat ... tttcttctagGGGACACTTAATGATGGAAGAGTCATTGCTGTGAAACAACTATCTGTGGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attggaactaaatcctttatttaagagaatattatttttcttttctttcttctagGGGACACTTAATGATGGAAGAGTCATTGCTGTGAAACAACTATCTGTGGGATCCCATCAAGGAAAGAGCCAATTCATAACTGAGATTGCTACTATATCAG
aactaaa putative branch site (score: 2)
tattatttttcttttc putative PPT
taaatcctttatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgaatcaaatcctttttctaatactcaatattttgagactaatattggaactaaatcctttatttaagagaatattatttttcttttctttcttctagGGGACACTTAATGATGGAAGAGTCATTGCTGTGAAACAACTATCTGTGGGATCCCATCAAGGAAAGAGCCAATTCATAACTGAGATTGCTACTATATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - -caaatcc