Sequence
atgc intronic sequence ATGC exonic sequence...aaatttgttgtgttataaaaaaatgtccaaaagcatttgattatcgagtcaaggacactatgcaaactagctctgattgatgcttttttgctttgagcagTCATTGTACTTGTATTGCTTGGGTTCCTGGAGGTGATGGTGCCTTTGTTGTAGGTCATGCTGATGGGAATTTGTAT
Basic information
species | Glycine max |
transcript | GLYMA13G20240.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 4
aaatttgttgtgttataaaaaaatgtccaaaagcatttgattatcgagtcaaggacactatgcaaactagctctgattgatgcttttttgctttg-agcagTCATTGTACTTGTATTGCTTGGGTTCCTGGAGGTGATGGTGCCTTTGTTGTAGGTCATGCTGATGGGAATTTGTAT------------
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-agttcgtttttaagtaggttaagttgaaacatgaatcaattttggcgtcatgactcttgccttctctaagtttaaaataaagtttgttgctttgtaacagTCGTTGCACTAGTATTTCTTGGGTGCCTGGAGGTGATGGAGCATTTGTCGTTGCTCATGCCGATGGCAATTTGTATGTGTATGAGAAG
upper sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 4
aaatttgttgtgtta-taaaaaaatgtccaaaagcatttgattatcgagtcaaggacactatgcaaactagctctgattgatgcttttttgctttgagcagTCATTGTACTTGTATTGCTTGGGTTCCTGGAGGTGATGGTGCCTTTGTTGTAGGTCATGCTGATGGGAATTTGTAT------------
| | || | | | | | | || | |||| | | | ||| || | | | ||| ||||||| | ||| | |||||| |||| |||||||| |||||||||||||| ||||||||| | |||||| ||||| ||| ||||
ataactgaaatctggctgagattccttttccgagaacaaaattactttat-atgttttttatccacttcaagaataagattaagtttgttgcttttaacagCCGCTGTACTAGTATAGCTTGGGTGCCTGGAGGTGATGGATCCTTTGTTGCTGCTCATGCCGATGGAAATCTGTACGTATATGAAAAG
upper sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 3'ss of exon 4
aaatttgttgtgttataaaaaaatgtccaaaagcatttgattatcgagtcaaggac-actatgcaaactagctctgattgatgcttttttgctttgagcagTCATTGTACTTGTATTGCTTGGGTTCCTGGAGGTGATGGTGCCTTTGTTGTAGGTCATGCTGATGGGAATTTGTAT------------
| | | | | | | || ||| | || | || | | | | | | | | || ||| ||| | || | ||||||| | ||||| ||||| |||| ||||||||||| || ||||| | |||||||||||| ||||||||
-tctgaataaggactttcagatgcattcagttccatgcaagtagaagtttaatatttagttagtaggtttaaccaagtaaactacttcttgtttttaatagCCGTTGTACTAGCATTGCATGGGTCCCTGATGGTGATGGTGCTTTCGTTGTTGCTCATGCTGATGGAAATTTGTACGTGTATGAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtcaaggacactatgcaaactagctctgattgatgcttttttgctttgagcagTCATTGTACTTGTATTGCTTGGGTTCCTGGAGGTGATGGTGCCTTTGTTGTAGGTCATGCTGATGGGAATTTGTAT
gattgat putative branch site (score: 4)
tgcttttttgcttt CT-rich tract
tttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatttgttgtgttataaaaaaatgtccaaaagcatttgattatcgagtcaaggacactatgcaaactagctctgattgatgcttttttgctttgagcagTCATTGTACTTGTATTGCTTGGGTTCCTGGAGGTGATGGTGCCTTTGTTGTAGGTCATGCTGATGGGAATTTGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - -tgttgtg
- - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg