Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtcatattgacatgttttgtacttttattatattctcaaggtatgaaaatcagctatgttgagttctggttacttaatgggcaaatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
Basic information
species | Glycine max |
transcript | GLYMA01G02480.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 5
gtgtgtcatattgacatgttttgtacttttattatattctcaaggtatgaaaatcagctatgttgagttctggttacttaatgggcaaat--gcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
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---------------gtatataagctataaacaccattattgaagcttaaaagtt--ctctcttgattcatcac-actgacaagccattttgttagGGTCATGAAAATGCTTCGGCTGAAAACGGACCATGGATCATCACATTGGATGCGCCAAGCTATATTGCTGTTATGCAGCATGCACGGAACAGAGCACTTC
upper sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgtgtca-tattgac---atgttttgtacttttattatattctcaaggtatgaaaatcagctatgttgagttctggttacttaatgggcaaatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
|| ||| |||| || | | | | || || || || | | | | || | |||| | || || || ||| || | | |||| ||||||||||| || ||||||||||| |||||||| |||||| | ||||||||||||| | || |||| |||||||||||| |||||| || |||
--gtatcaatattaactgaaagatatataaagtt-ccatgtttcgttatttttttagtaaggtttgttaatttttgctt-cttgatatgtgacactagGGCCATGAAAATGCAACTGCTGAGAATGGACCATGGATCATTACACTGGATGCTCCTAGTTATCTTCCTGTCATGCAACATGCTAAAAACCGTGCTCTGC
upper sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgtgtcatattgacatgttttgtacttttattatattctcaaggtatgaaaatcagctatgttgagttctggttacttaatgggcaaatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
|| | |||| | | ||| || || | || || || | |||||| ||| ||| | || | |||| ||||||| ||| || ||||| | ||| |||||| | |||||| | ||||||||||||| | || | |||||||||||||| ||||| || |||
--gtataatatctgaaagatttataaagtt-tcatgttgatttacattgggtttttaagttgttga-ttcgtcttaat--atatatgacccaagGGCCATGAAACTGCAACTGCTGACACTGGACCATGGCTCATTACACTCGATGCTCCTAGTTATCTTCCCGTTATGCAACATGCCAAAAACCGAGCTCTGC
upper sequence: GLYMA01G02480.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 5
-----------------gtgtgtcatattgacatgttttgtacttttattatattctcaaggtatgaaa-atcagctatgttgagttc--tggttactta-----atgggcaaatgc---agGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
|| ||| ||| || || || | || | |||||| | || || || || | || | || |||| || ||| | |||||||| || |||| || |||||||||||||| |||||||||||||| |||| ||| || ||| || |||||||||||||||||| |||||||| ||||
gtatttttagctgatttgtagctca-atttttttgcttgttaatccatttccttcctcaagtccagtaatattggcaattctcttctcattttttgcttatgctcatctacaatcacttcagGGGCATAAAGATGCTACTGCTGAGAATGGGCCTTGGATAATTACATTGGATGGTCCAAGCTTTCTTTCTGTTATGCAACATGCTCAAAACCGTTCCTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaggtatgaaaatcagctatgttgagttctggttacttaatgggcaaatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
acttaat putative branch site (score: 4)
tatgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtcatattgacatgttttgtacttttattatattctcaaggtatgaaaatcagctatgttgagttctggttacttaatgggcaaatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT