Sequence
atgc intronic sequence ATGC exonic sequence...caatgttacagctttgtcattgatgcatatgaagctatatttttggggttactctatgttgtattgcaattaaatcacaaataaattatatatgttacagATGTCAAATAGCAGTTCATCAAGAATGCTATGGAGCAAGAAATGTCCGAGATTTTACATCTTGGGTTTGTAAAGCTTGCGAAAGACCTGACATCAAGCGG
Basic information
species | Glycine max |
transcript | GLYMA04G41500.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 11
--caatgttacagctttgtcattgatg-catatgaagctatattt-ttggggttactctatgttgtattgcaattaaatcacaaataaattatatatgttacagATGTCAAATAGCAGTTCATCAAGAATGCTATGGAGCAAGAAATGTCCGAGATTTTACATCTTGGGTTTGTAAAGCTTGCGAAAGACCTGACATCAAGCGG
| | | | | || | | | ||||| || || || | || | | | ||||| | ||| | | ||| |||||| ||||||||||| ||||| ||||||||||| || ||| |||| || ||||| || || ||||| |||||||| ||||| ||||| || |||||||||
ttgttttctgtggatcactttatggcgacttgtgaagtatcatccattatcattgtttcataa-gcaacttagataaatgtttctttcattttct-tgt--cagATGCCAAATAGCAGTGCATCAGGAATGCTATGGCGCTAGACATGTTCGTGATTTCACCTCATGGGTCTGTAAAGCATGCGAGAGACCAGATATCAAGCGG
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 11
caatgttacagctttgtcattgatgcatatgaagctatatttttggggttactctatgttgtattgcaattaaatcacaaataaattatatatgtta----cagATGTCAAATAGCAGTTCATCAAGAATGCTATGGAGCAAGAAATGTCCGAGATTTTACATCTTGGGTTTGTAAAGCTTGCGAAAGACCTGACATCAAGCGG
|| || | | | | | || |||| | || | | || || | | ||| ||| || | | | | || |||||||||||||||||||||||| ||||||||||| | ||||| || || || || ||||| ||||| || ||||| ||||| | |||||| ||||| ||
--ttgctattattattcagaaaaaaaaaacgagaaaatatctgacttgtgaagc-atatt-tggtatcattgaattttaagtcttctgttccttttctcctcagATGTCAAATAGCAGTTCATCAGGAATGCTATGGGACGAGAAACGTTCGTGACTTCACATCATGGGTCTGCAAAGCCTGCGAGACACCTGAGATCAAACGA
upper sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 12
caatgttacagctttgtcattgatgcatatgaagctatatttttggggttactctatgttg-tattgcaattaaatcacaaataaatt----atatatgttacagATGTCAAATAGCAGTTCATCAAGAATGCTATGGAGCAAGAAATGTCCGAGATTTTACATCTTGGGTTTGTAAAGCTTGCGAAAGACCTGACATCAAGCGG
| || || | ||| ||| | || | || |||| | || | || || ||||| || || | || || | | | ||||||||||||||| || |||||||| || ||||| ||||||||||| || ||||| || || |||||||| | ||| || |||| |||||| | |||||
----accaaagaattttttttgttgcctg-gagattttactttttgagtactccaataacactaaatgaattatattacttttttttttttaatttctataccagATGTCAAATAGCCGTCCATCAAGAGTGTTATGGGGCAAGAAATGTTCGGGATTTCACTTCATGGGTTTGCAGAGCATGTGAAACACCTGATGTTGAGCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggttactctatgttgtattgcaattaaatcacaaataaattatatatgttacagATGTCAAATAGCAGTTCATCAAGAATGCTATGGAGCAAGAAATGTCCGAGATTTTACATCTTGGGTTTGTAAAGCTTGCGAAAGACCTGACATCAAGCGG
tattgcaattaaatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatgttacagctttgtcattgatgcatatgaagctatatttttggggttactctatgttgtattgcaattaaatcacaaataaattatatatgttacagATGTCAAATAGCAGTTCATCAAGAATGCTATGGAGCAAGAAATGTCCGAGATTTTACATCTTGGGTTTGTAAAGCTTGCGAAAGACCTGACATCAAGCGG
caatgtt
- - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - -tttgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa