Sequence
atgc intronic sequence ATGC exonic sequence...ctatattgtatatgttagatggttagcatatctgtttttatacaaatacaaattggggaacaaatgatgaggttatggattttattttatttgtttccagCAACTTGTTTCAGAAAAAGATCTGATAGTAAGGGAAGAAGCATGCCGCATTGGTCTTCTTTTTGGTGGTTTCACTGGATCTTATCATGCTCTTAGATGCT
Basic information
species | Glycine max |
transcript | GLYMA20G34070.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g31260.1 (Oryza sativa), 3'ss of exon 1
ctatattgtatatgttagatggttagcatatctgtttttatacaaatacaaattggggaacaaatgatgaggttatggattttattttattt----gtttccagCAACTTGTTTCAGAAAAAGATCTGATAGTAAGGGAAGAAGCATGCCGCATTGGTCTTCTTTTTGGTGGTTTCACTGGATCTTATCATGCTCTTAGATGCT
| | | | | | | || || | ||||| | ||| | || | | ||||| | || || || ||| | | ||| ||| ||| |||||||| ||||| || |||||||| ||||| ||||| ||||| ||||| | || | |||||||| || ||||||||||| |||||||| ||| |||| |
ccaaact-tccctttctgacaaatat--ttactgttctactactagtatactacaaagttcaaataa-gatgtcattgatataactttcttttctaatttgcagCAACTGGTTTCGGAGAAAGATCTAATAGTGAGGGAGGAAGCTTGCCGGGTAGGATTACTTTTTGGAGGATTCACTGGATCATATCATGCACTTCGATGTT
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G175799_T02 (Zea mays), 3'ss of exon 1
ctatattgtatatgttagatggttagcatatctgtttttatacaaatacaaattggggaacaaatgatgaggttatggattttattttattt--gtttccagCAACTTGTTTCAGAAAAAGATCTGATAGTAAGGGAAGAAGCATGCCGCATTGGTCTTCTTTTTGGTGGTTTCACTGGATCTTATCATGCTCTTAGATGCT
|| | | | || | | || ||| | | | | | | || | || || || | | | ||| ||| |||||||| ||||| || |||||||| |||||||| || ||||| ||||| | || | |||||||| || ||||||||||| |||||||| ||| |||| |
ctgcttcgaacccgtgacctagt-ggcacagcgagacaactcttaccatagcactaggc-ctgcccatctatatactcatctgaatacattctgatttacagCAACTGGTTTCGGAGAAAGATCTTATAGTAAGAGAGGAAGCTTGCCGGGTAGGGTTGCTTTTTGGCGGATTCACTGGATCATATCATGCACTTCGATGTT
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G51150.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------------------------ctatattgtatatgttagatggttagcatatctgtttttatacaaatacaaattggggaacaaatgatgaggttatg---gattttattttatttgt-------ttccagCAACTTGTTTCAGAAAAAGATCTGATAGTAAGGGAAGAAGCATGCCGCATTGGTCTTCTTTTTGGTGGTTTCACTGGATCTTATCATGCTCTTAGATGCT
|| | | || |||| || || | |||||| | || | | ||| | | | | || | ||| |||| | | || || ||||||||||||||||| |||||| ||||||| ||||| |||||||| || |||||||| ||||||||||| || ||||| || |||||||| ||||||||||
gtgaggaattgatgaattggaatttgtttttgtggcaatttctggagatttagagtcttacgagtctctgcttta-gtgttccat--ttgatacggttgttttgaaactatggccaatgtgttattgacttatcattgtatatgcgattcactcacacgtgaacaatggttgcagCAACTTGTTTCAGAGAAAGATTTGATAGTTAGGGAGGAAGCATGTCGTATTGGTCTACTTTTTGGTGGCTTTACTGGCTCGTATCATGCCCTTAGATGCT
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0039g02700.t01 (Vitis vinifera), 3'ss of exon 1
ctatattgtatatgttagatggttagcatatctgtttttatacaaatacaaattggggaacaaatgatgaggttatggattttattttatt-tgtttccagCAACTTGTTTCAGAAAAAGATCTGATAGTAAGGGAAGAAGCATGCCGCATTGGTCTTCTTTTTGGTGGTTTCACTGGATCTTATCATGCTCTTAGATGCT
| | | | ||||| | |||| | || | | || || || | || ||| | || | || ||| | ||| ||||||||||| ||||| |||||| |||||||||| ||||||||||| || ||||| | |||||||||||||| |||||||| |||||||| || |||| |
ggttgggggaggggaaagatgctacgcattatgcatattctggatatgcatctttattcatggctgttgat-tagtgtgaaaaacttcattatatttgcagCAACTTGTCTCAGAGAAAGATTTGATAGTAAGAGAAGAAGCATGTCGTGTTGGTTTACTTTTTGGTGGTTTTACTGGATCCTATCATGCCCTCCGATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacaaattggggaacaaatgatgaggttatggattttattttatttgtttccagCAACTTGTTTCAGAAAAAGATCTGATAGTAAGGGAAGAAGCATGCCGCATTGGTCTTCTTTTTGGTGGTTTCACTGGATCTTATCATGCTCTTAGATGCT
ttttatttgtttcc CT-rich tract
ttatggattttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctatattgtatatgttagatggttagcatatctgtttttatacaaatacaaattggggaacaaatgatgaggttatggattttattttatttgtttccagCAACTTGTTTCAGAAAAAGATCTGATAGTAAGGGAAGAAGCATGCCGCATTGGTCTTCTTTTTGGTGGTTTCACTGGATCTTATCATGCTCTTAGATGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - -gatggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - ttgggga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgag