Sequence
atgc intronic sequence ATGC exonic sequence...cttttggcaaaatagaaatgcttttaattgccttattttctgcctatttatgacatgaatgcagcattctcacatttattttgtcttttgttgcatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAATATGG
Basic information
species | Glycine max |
transcript | GLYMA16G00210.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 4
cttttggcaaaatagaaatgcttttaattgccttattttc-tgcctatttatgacatgaatgcagcattctcacatttattttgtcttttgttgcatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAATATGG
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-taggaccaaggcgtgaacttctacacttgatagatcttcatattctttaaccccagtaatccactgcttgttatcttagtgcacaccttattgcatccagGGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAAGAAGGGATATCAGTCATAAAGCCTATGGGTATTATGATATTTAACATGG
upper sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G098039_T01 (Zea mays), 3'ss of exon 4
--cttttggcaaaatagaaatgcttttaattgccttattttctgcctatttatgacatgaatgcagcattctcacatttattttgtcttttgttgcatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAATATGG
|| | ||| | ||| | || | ||| || || | || | | || | | || |||||| |||||||||| ||||||||||||||| | || || |||||| | || || || || |||||| | || || || || | || |||||| | || || ||||
gttaaatgattattcagaccaatcctacattagaat-ttctttgcttaaggattttgattttcttttatgtttgccaacatcg-atatctttctgcatccagGGTTTTGTCGAGGACCAATTTGGCCTTGGGTTGATTGCTCGTGCGGTGGAAGAAGGGATATCTGTCATAAAGCCTTCAGGTATTATGGTATTCAACATGG
upper sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 4
cttttggcaaaatagaaatgcttttaat--tgccttattttctgcctattta--tgacatgaatgcagcattctcacatttattttgtcttttgttgcatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAATATGG
|| | | ||| | | | ||| | | | ||| | || | | || |||| | | | || | | | || |||||||||| || || || |||||||||||||| ||||| || |||||||| || || ||| | || |||||||| | || |||||||| ||||| ||||
---ttaatttactctaaaaggtgtaaatgatagaccaggtactggaaactttgttaaagtggatgctctacctgtgc-ctgatgaaatttgtatccatattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
upper sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 5
cttttggcaaaatagaaatgcttttaattgcctta--ttttctgcctatttatgacatgaatgcagcattctcacatttattttgtc-ttttgttgcatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAATATGG
| | | || || | | ||| | | ||| ||||| | | | | | |||| | | ||| | || || | ||||||||||| ||||| || ||||| || ||| |||||||||| ||||||||||| || ||||| || |||||||||| || ||||||||||| |||||||
---tccaaagggaaaaattgttatccattacaatgggtttgttgcctttcttcttctttttcctctctctctctctctcttttcacaatctttttctctatagGGTTTTGTCGAGGATCAGTTTGGATTGGGTCTAATTGCTAGAGCAGTTGAGGAAGGAATAGCTGTCATCAAACCAATGGGCATTATGATCTTCAATATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatgacatgaatgcagcattctcacatttattttgtcttttgttgcatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAATATGG
ttctcac putative branch site (score: 2)
ttttgtcttttgtt putative PPT
atttattttgtctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttggcaaaatagaaatgcttttaattgccttattttctgcctatttatgacatgaatgcagcattctcacatttattttgtcttttgttgcatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAATATGG
cttttgg
- - - - - - - gaaatgc
- - - - - - - - - - - - - - tgcctta
- - - - - - - - - - - - - - - - - - - -ctgccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattct