Sequence
atgc intronic sequence ATGC exonic sequence...ctattctttatagtcattatgatttataattgaagtcgtcttgctattttaattaaataagctatctggtgtaattattctcaaaatattgtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGGATAGTTAGCAAACTACTTGTACTTC
Basic information
species | Glycine max |
transcript | GLYMA05G28950.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 1
----ctattctttatagtcattat-gatttataattga-agtcgtcttgctattttaattaaataagctatctggtgtaattattctcaaaatattgtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGGATAGTTAGCAAACTACTTGTACTTC
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ttttctttgacatatacttacaattgacttgtcattaatacccatcaagttatc--agctagacatgctcta----atcattgttttatattccgaatgagttcagGCACACGCAGCTTCTGCGATTCTAAACTTCAGCGAAAACTGCAGGCCTGATATTTTGACACCATACTTGGATGGGATAGTTGGGAAACTACTGTCATTGC
upper sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 1
ctattctttatagtcattatgatttataattgaagtcgtcttgctattttaattaaataagctatctggtgtaattattctcaaaatattgtctaca----cagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGGATAGTTAGCAAACTACTTGTACTTC
| | | ||| | | || || | | | | | | | | | || || | | || | |||| ||||| |||||||||||||| ||||| |||| |||||||| || ||||||| ||||||||| || || ||||||||||||| |||||| | ||||| || | | |
-tggtttacataaagtcgagggcttgctatatctgctct-tcatcaaacacaccagctgaccaataaggcat--tctctcatattttatttcctacatgttcagGCACATGCTGCATCAGCTATTCTGAACTTCAGTGAAAACTGCAGACCTGATATTTTGACACCATACTTGGATGTAATAGTTGGGAAACTTCTATTGTTAC
upper sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 2
ctattctttatagtcattatgatttataattgaagtcgtcttgctattttaattaaataa-gctatctggtgtaattattctcaaaatattgtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGGATAGTTAGCAAACTACTTGTACTTC
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----------------------gtaagatcccctgtttctctgtgaatataatcttctaacactttctaaagcagta--ccttgtgaccttttc-atgtagGCTCATGCTGCTTCAGCAGTACTCAACTTCAGTGAAAATTGTACTCCTGAAATATTGTCACCTTATTTAGACGGAGTAGTGAGCAAGTTACTTGTGCTAC
upper sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 2
ctattctttatagtcattatgatttataattgaagtcgtcttgctattttaattaaataagctatctggtgtaattattctcaaaatatt---gtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGGATAGTTAGCAAACTACTTGTACTTC
|| | ||| || |||| || || | | ||| | | ||| || ||| | || | | | ||| | || | | ||||||||||||||||||||| || ||||||||||| ||||||||||| || ||||| ||||||||||| || ||||| || ||| ||||| |||| |||||||
agtggctcagtgctcaagattattt-tatttttaattttctcgttctttactttgaatga--tagttaataatggttttccattgttgttcgaatttctacagGCACATGCTGCTTCAGCTGTGCTCAACTTCAGTGAGAACTGCACTCCAGATATTTTAACGCCATATTTAGATGGAATTGTTGGCAAATTACTAGTACTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttaattaaataagctatctggtgtaattattctcaaaatattgtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGGATAGTTAGCAAACTACTTGTACTTC
ttttaat putative branch site (score: 3)
tgtaattattctcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctattctttatagtcattatgatttataattgaagtcgtcttgctattttaattaaataagctatctggtgtaattattctcaaaatattgtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGGATAGTTAGCAAACTACTTGTACTTC
- - - - - - - - - - - - - - - - - - - -cttgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctggtg