Sequence
atgc intronic sequence ATGC exonic sequence...ttttccttgatttttttggtttgcaagttgtttgagcaatcactgtgctcaaccctcaaataaggattcttactaatgattgataaatctatcaatggagCTGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGATTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAAAAAA
Basic information
species | Glycine max |
transcript | GLYMA15G12970.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G12970.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 3'ss of exon 7
ttttccttgatttttttggtttgcaagttgtttgagcaatcactgtgctcaaccctcaaataaggattcttactaatgattgataaatctatcaatggagCTGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGATTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAAAAAA
| ||| ||| | || | || || | |||| | | || | || || |||| | || | ||| || ||| |||||||| |||||||| || || ||||||||||| || ||||| | |||||||||||| |||||||| | |||||||| ||| ||||||
------gtaattgccttgttctgttataaagtt---cattagatgtgacc--tttttgaacttgcatctgtattaat-actgttttatcc-ccagTGGTGCTGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCA-----
upper sequence: GLYMA15G12970.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0568g00010.t01 (Vitis vinifera), 3'ss of exon 7
ttttccttgatttttttggtttgcaagttgtttgagcaatcactgtgctcaaccctcaaataaggattcttactaatgattgataaatctatc-aatggagCTGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGATTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAAAAAA
|| || | | ||| ||| | || | || ||| | | ||||| | || ||| ||| | || | | || | ||| || |||||||||||||||||| ||||||| ||||||||| || || || |||||||||||||| ||||| |||||||| | |||||||||||||
-gttgtttattatcttttgttgtagtggtggtaaagtaattcatat---------ctaaatacaggagctgact--tgagctaaaattttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA-----
upper sequence: GLYMA15G12970.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s1206g00020.t01 (Vitis vinifera), 3'ss of exon 3
ttttccttgatttttttggtttgcaa-gttgtttgagcaatcactgtgctcaaccctcaaataaggattcttactaatgattgataaatctatc-aatggagCTGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGATTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAAAAAA
| || ||| | || |||| | | |||| || ||| | | ||||| | || ||| ||| | || | | || | ||| || |||||||||||||||||| ||||||| ||||||||| || || || |||||||||||||| ||||| |||||||| | |||||||||||||
--gttgtttattatctttttttgtagtggtgttaaagtaattcatat---------ctaaatacaggagctgact--tgagctaaaattttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA----- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctcaaccctcaaataaggattcttactaatgattgataaatctatcaatggagCTGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGATTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAAAAAA
taatgattgataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttccttgatttttttggtttgcaagttgtttgagcaatcactgtgctcaaccctcaaataaggattcttactaatgattgataaatctatcaatggagCTGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGATTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAAAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- ttccttg
- - - - - - - - - - -tgcaagt
- - - - - - - - - - - - - - - - - - caatcac
- - - - - - - - - - - - - - - - - - - - - - - - tcaaccc