Sequence
atgc intronic sequence ATGC exonic sequence...tctattgagctttgaattccttttctatctcaccatagtatattgcactcttaatattttcaattcttgtaatttgtactcacgaccttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA
Basic information
species | Glycine max |
transcript | GLYMA12G01380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 3
tctattgagctttgaattccttttctatctcaccatagtatattgcactcttaa---tattt-tcaattcttgtaatttgtactcacg-accttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA
| | |||||| | ||| | | | | | | | | || || | ||| | ||| | ||| ||| || | || || ||| || |||||||||| || |||||||| ||||||||||| || |||||||| ||||| |||||||| ||||| || |||||||| || || |||||| | | ||||
---agttctgtttgaagactgtttacaagttatagttttttctctctctgttcaaggtatatgtcatgttttgagattaataataacccactttctgttc--cagGAATGGTTGCAGCTTTAACTAATGAGAGTGCAACAAGCAAGTCGGTGTATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTCACAGA
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
tctattgagctttgaattccttttctatctcaccatagtatattgcactcttaatattt--tcaattcttgtaatt-tgtactcacgaccttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA
| ||||| | | ||| |||| | | || ||| | || | || | || ||| | | | | || | | || |||| ||||| || ||| |||||||||||||||| |||||||| || || |||||||||| ||||||||||| ||||||| ||||| || || |||| |||
---gctatgctttacgtcgcgttttaatcttgtcgtggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
--tctattgagctttgaattccttttctatctcaccatagtatattgcactcttaatattttcaattcttgtaatttgtactcacgaccttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA
|| ||| | ||| | || || | || || | | | || || || | || | | | | | || | |||||||||| || ||||||||||| |||||||| || ||||| || || || |||||||| ||||| || |||||||| || || |||||| | || ||||
gacctgaggagtgctactcagaccacctaaccaactcagctagag-gccctttcgcgagtaccagtt-ttatcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 3
-tctattgagctttgaattccttttctatctcaccatagtatattgcactcttaatattttcaattcttgtaatttgtactcacgaccttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA
| | ||| |||| | || || | | | | | | ||| |||||| || || || | |||| |||||||| || |||| || |||||||| |||||||| || || |||||||| | ||||||||||||||||| | || || || || ||| |||
gtgcagtgaactttattctatgcacatagcttggcgctcagtgacacccccaagtagcctatgatttcatcaatttgc-tgaacattctgatatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACTTTGCACTTTGCACATCTGAGATGATCTACATCACACACCTTCTGGAAGA
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
----tctattgagctttgaattccttttctatctcaccat--agtatattgcactcttaatattttcaattcttgtaatttgtactcacgaccttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA
||| || | | | ||| ||| || | || |||||| | | || |||| | | || |||| | | || |||||||||||||||| ||| |||| |||||||||||||||||||| |||||||||||||| || || ||||| |||||||||||||| || ||||| || ||||
gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgg--gttggaatttgta-agttcttactttgaatttgca---taacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGAMapped 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|58014578|gb|CX701320.1|CX701320EST: TACTCATGAAGTTATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG GAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACT
genomic: TACTCATGAAGTTATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaaaaacta ... aatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactcttaatattttcaattcttgtaatttgtactcacgaccttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA
tactcac putative branch site (score: 1)
ttaatattttcaattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctattgagctttgaattccttttctatctcaccatagtatattgcactcttaatattttcaattcttgtaatttgtactcacgaccttcaatttaacagGAATGGTAGCCGCTTTAACAAATGAGAGTGCCACCAGCAAGTCAGTGTACTTTGCTCACTGCACATCTGAGATGATTTTTATAACTCATCTATTGGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - tgaattc
- - - - - - - - - - - - - - -tcaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacgacc