Sequence
atgc intronic sequence ATGC exonic sequencegtattagaaaactttctcctttttctgaaaaatataataacttccagcaaaaatactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAGGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGACGCCTTCCCCATTTCTC
Basic information
species | Glycine max |
transcript | GLYMA04G26840.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 3'ss of exon 5
-----------------------gtattagaaaactttct-----cctttttctgaaaaatataataacttccagcaaaaat----actttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAGGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGACGCCTTCCCCATTTCTC
|| || || | | | ||| ||| | | || || | ||| | ||| | | ||||| || |||||||||||||||||||| || ||||||||||||| ||||| ||||| |||||| |||||||| |||||||| || ||| ||||| |
tccttatctatgtgtatgctttctgatggctaagctgtatgccaacttttatctttgatacttagaaatcgttgactaaatttttcgcttcactattcagGAAGAAAGAGATGCAATTTTGGCCAAAATAGAAGTTTCACAGGTTCATTTGGAATTGCTGAAGCAAACAAATGTTCTCAATGATGCATTCTATATTTCAC
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g44200.1 (Oryza sativa), 3'ss of exon 6
-----------------------gtattagaaaactttctcctttttctgaaaaatataataactt--ccagcaaaaa-------tactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAGGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGACGCCTTCCCCATTTCTC
||| || ||| | | | | | | || | || | ||| || | | | | | ||||| || |||||||| ||||||||||||| |||||||| |||| ||| ||||||| || |||||||||||||| |||||||| || ||| ||||| |
atattataatatgtattggttccttatacataagcttcataatgtctgggctgtttgcaagcatttgcctgtcaataactcatttttttgtcactttcagGAAGAAAGAGATGCGGTTTTGGCCAAGATAGAAGTTTCGCAGGTTCATCTAGAATTGTTAAAGCGTACAAATGTTCTCAATGATGCATTCTATATTTCAC
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 5
--------------------------------gtattagaaaactttctcctttttctgaaaaatataataacttccagcaaaaatactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAGGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGACGCCTTCCCCATTTCTC
||| | | | | ||||||| || | | | | ||||||| | || ||||| || ||||||||| |||| |||||||| |||||||| |||| ||||| ||| | ||||||||||| ||||| |||||||| || ||| || || |
attttagttatctatatgcaatattttcttacactttaatagtttgccactattttctgtgctattcattttggtatattaaaaatatcacacttttcagGAAGAAAGAGATGCAGTTTTTGCCAAGATAGAAGTTTCTCAGGTTCATTTGGAACTGTTGAAGCGTACTAATGTTCTCAATGATGCATTCTATATATCAC
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G61710.3 (Arabidopsis thaliana), 3'ss of exon 5
---------------------gtattagaa-aactttctcctttttctgaaaaata-----taataacttccagcaaaaa-----tactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAGGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGACGCCTTCCCCATTTCTC
| | | || | ||| |||| || | || | | | | || || ||| | || ||||||||| |||||||||||||| ||||| ||||||||||||||||| ||||||||||| ||||| || |||||||| || | ||| |||||||||||
attgtggtattagtagccatagcacttgattaggtttaggctttatcagtgtaacactcgtttcttagatctagtgtaaaagatatgtctttgttaacagGAAGAGAGAGATGCAATCTTGGCAAAGATTGAAGTTTCACAAGCACATTTAGAGTTATTAAATAAGACAAATGTACTTATTGATGCCTTCCCCATACGGA
upper sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------gtattagaaaactttctcctttttctgaaaaatataataacttccagcaaaaatactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAGGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGACGCCTTCCCCATTTCTC
| |||| | || || |||| ||| | ||| | || | |||| | || | ||||||| ||||||||||||||| |||||||||||||||| |||||||||||| |||| || |||||| | || ||||| || ||||| ||||||||||||| |
gtatgttgctggtatataaaccgttgctgctctttttagtagttttactgctttgtct-atgaatctttcaattgtttacaaagagttttctgtcaacagGAAGAGAGAGATGCAATTCTGGCCAAGATTGAAGTGTCACAGGCACATCTAGAGTTGTTGAAGAGAACTAATGTACTGAATGATGCCTTCCCCATTTGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcctttttctgaaaaatataataacttccagcaaaaatactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAGGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGACGCCTTCCCCATTTCTC
tttttctgaaaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattagaaaactttctcctttttctgaaaaatataataacttccagcaaaaatactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAGGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGACGCCTTCCCCATTTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC