Sequence
atgc intronic sequence ATGC exonic sequencegtatccccctctccccttcatatattaattttaattttaagtttttctgtttatctttcagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
Basic information
species | Glycine max |
transcript | GLYMA13G06660.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 1
-------------------------------gtatccccctctcccct-tcatatatta--------attttaattttaagtttttctgtttatctttcagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
||| | | | | | | |||||||| |||| | | || ||| |||| | ||| ||||||| |||||||| || ||||||||||| |||||||||||||| ||||| || | | ||||| || ||||||||||||
ttcaggtttgcaaattgcagggtagccacatttatttgcttttactttgtgatatattatacatttttttttgttgtgaaatttgcctgtctctctg-cagAAGCATATGATCCTCTCGATCCAAATGGGAATATCACAATCAAGTGGGACATCACACAGTGGACCCCAGATGGCTATGTT
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 1
---------------------------gtatccccctc---tccccttc---atata--ttaat-tttaattttaagtttttctgtttat---ctttcagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
|| | || | || || || || ||||| |||||| | | | ||| ||| | ||| |||||||||||||| | || ||||||||||| || |||||||| |||||||| |||| ||||| |||||||| || |||
ccgcgaatttcttattagttgtgtggtgtgtaccttttaaatcggaatcgggatgtaacttaatgcttaattcatattctctctcttttttttcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g32110.1 (Oryza sativa), 3'ss of exon 1
---------------------------------gtatccccctctccccttcatatatta--attttaattttaag----tttttctgtttatctttcagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
|| |||| | || | | | | | || || || | | ||||| | || |||| |||| ||||||||| | || |||||||||||||| ||||| || |||||||| |||| ||||| |||||||||||||||
tcatggggcttattcatctgccgaactgctaatttacccccatttcgtttcccttgttcaggatcttgatatgcaactcttttttgttttcctcttgcagAGGCTTATGATGCGCTGGATCCAAATGGAAACATCACGATAAAATGGGACGTTATGTCGTGGACTCCTGATGGCTATGTT
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------gtatccccctctccccttcatat---attaattttaattttaagtttttctgtttatcttt-cagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
| | | | | | || ||| | || | | |||| | | ||| ||||||| |||||| | ||||||||| | || || || ||||| ||||||||| |||| |||||||| |||||||||||||||
ctacaaaccaaataattagtagttttaagattgaagcaatcacaatgtcggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G29810.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------gtatccccctctccccttcatatattaattttaattttaagtttttctgtttatctttc------agaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
|| | | | | | | || | | | | | ||| | ||||||||| ||||||||||||| ||||||||||| ||||||| || || || |||||||||||||| |||||||| |||||| |||||
tctattatcttaaccaattgataggaaaaagtcttaattttgtgtttgttctgttttctggttatgagctcacatgtttgagattatctttctaacacagAAGCTTATGATGCACTTGATCCATATGGAAACATTACTATAAAATGGGATATTATGAGCTGGACTGGTGATGGTTATGTG
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------gtatccccctctccccttcatatattaattttaattttaagtttttctgtttatc--tttcagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
||| |||| | || || | | | |||| |||| || |||||||||| |||||| |||| ||||| |||||||||||||| ||||||||||||||||| |||||||| || ||||||||||||
aatgttttctaatatctctattgtgtgtcagtgaaatatatatatttctcagaaaagggattgaagatttagccttatcttttgggtttctccttttcagAAGCCTATGATGCACTGGATCCCAATGGAAATATCACGATCAAATGGGATATTATGAGCTGGACTCCAGATGGCTATGTT
upper sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 1
---------------------gtatccccctctccccttca----tatattaattttaat--tttaagtttttctgtttatct------------ttcagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
| |||| | | || | || ||| |||| || | || || | ||| | | | ||||||| || ||| | ||||||||| | ||||||||||| ||||| |||||| | || |||||||| || ||||| ||||||
ccaaaaaaagaaaagattgaactctccctttatgaaatttaatgtcatgagaatcttaagaattgaggtattcatctttctttggtggatgtttctgcagAAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctccccttcatatattaattttaattttaagtttttctgtttatctttcagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
tttttctgtttatctt CT-rich tract
atatattaattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatccccctctccccttcatatattaattttaattttaagtttttctgtttatctttcagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA