Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaccactcttttccaaagtttcataattcctcgatttctccgtcgttgatgaatcaattttgattttgtcgtaaagGGTTATGCTTGTGGGTTTGGGAGGAAACAATGGATCAACTCTCACCGCTGGTGTGATTGCGAACAAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39800.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G31450.2 (Glycine max), 3'ss of exon 1
----------------------------gtaaaaaccact--cttttccaaagtttcataattcctcgattt-ctccgtcgttgatgaatcaattttgattttgtcgtaa-agGGTTATGCTTGTGGGTTTGGGAGGAAACAATGGATCAACTCTCACCGCTGGTGTGATTGCGAACAAAGA
||| ||| | | || || ||| || | |||| | | | |||||||| ||| | ||||| | ||||| ||||||||||| | ||| ||||||||||| ||||| ||||||| |||||| ||||| ||| |||
gttagtacgttctcatgtcctcctccccttaattacccttaattatttgaatttttttccatcttttaatttattgctttgttgatgatatggtttctttgttgtcttgctagGGTAATGCTTGTGGGGTGGGGTGGAAACAATGGCTCAACCCTCACCGGTGGTGTTATTGCTAACCGAGA
upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G02210.4 (Glycine max), 3'ss of exon 1
---------------------------------gtaaaaaccactcttttccaaagtttcataattcctcgatttctccgtcgttgatgaatcaatt--ttgattttgtcgtaaagGGTTATGCTTGTGGGTTTGGGAGGAAACAATGGATCAACTCTCACCGCTGGTGTGATTGCGAACAAAGA
|| | | | || ||| | || | | || | || | | | |||| |||||| | | | |||| ||||||||||||| ||| |||||||| || || || ||||||| |||||| ||||| |||| |||
gttagccttcacatcaacgtcatttttttatatatatatattattcgaaatcaagacgctttttttattttaattttttatcctgatttgtttaattggttgatta-attatca-gGGTGATGCTTGTGGGTTGGGGTGGAAACAACGGCTCTACCCTCACCGGTGGTGTTATTGCTAACAGAGA
upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G14670.1 (Glycine max), 3'ss of exon 1
--------------------------------------------gtaaaaaccactcttttccaaagtttca----taattcctcgatttctccgt------cgttgatgaatcaattttgattttgtcgtaaagGGTTATGCTTGTGGGTTTGGGAGGAAACAATGGATCAACTCTCACCGCTGGTGTGATTGCGAACAAAGA
|| || | || | | ||| | || || || || | | | | ||| ||| ||| | ||||| ||||| ||||||||||| | ||| ||||||||||| ||||| ||||| | |||||| ||||| ||| |||
gttagtacgttctcatgtcctcctccccttagttacccttaatagtttgaatgtatattcttttgaattttatttttattttttccatcttttattttattgctttgttgatatggtttctttgttgtctgctagGGTAATGCTTGTGGGGTGGGGGGGAAACAATGGCTCAACCCTCACTGGTGGTGTTATTGCTAACCGAGA
upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 1
--------------------------------------------gtaaaaaccactcttttccaaagtttcat----aattcctcgatttctccgt------cgttgatgaatcaattttgattttgtcgtaaagGGTTATGCTTGTGGGTTTGGGAGGAAACAATGGATCAACTCTCACCGCTGGTGTGATTGCGAACAAAGA-------------------------------
|| || | || | | ||| || | || || || | | | | ||| ||| ||| | ||||| ||||| ||||||||||| | ||| ||||||||||| ||||| ||||| | |||||| ||||| ||| |||
gttagtacgttctcatgtcctcctccccttagttacccttaatagtttgaatgtatattcttttgaattttatttttattttttccatcttttattttattgctttgttgatatggtttctttgttgtctgctagGGTAATGCTTGTGGGGTGGGGGGGAAACAATGGCTCAACCCTCACTGGTGGTGTTATTGCTAACCGAGAGTTAGTTTCATCTTCAATTCCTAATCATTAA
upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 1
---------gtaaaaaccac-tcttttccaaagtttcataattcctcgatttctccgtcgttgatgaatcaattttgattttgtcgtaaagGGTTATGCTTGTGGGTTTGGGAGGAAACAATGGATCAACTCTCACCGCTGGTGTGATTGCGAACAAAGA
||| ||| | | || | || |||| | | ||||| ||| | ||| |||| |||| |||| | ||||||||||||||||||| |||||||||||| || ||| ||||||| | |||||| ||||| || ||
gttggcatcttaacaactgtgtttctttccaattttc----ctttttgattt-tccat-gtttccgaattgatttctgtttt--tgactagGGTTATGCTTGTGGGTTGGGGAGGAAACAACGGCTCATCTCTCACTGGTGGTGTAATTGCCAATCGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cataattcctcgatttctccgtcgttgatgaatcaattttgattttgtcgtaaagGGTTATGCTTGTGGGTTTGGGAGGAAACAATGGATCAACTCTCACCGCTGGTGTGATTGCGAACAAAGA
ttttgat putative branch site (score: 4)
ttttgtc CT-rich tract
aatcaattttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaccactcttttccaaagtttcataattcctcgatttctccgtcgttgatgaatcaattttgattttgtcgtaaagGGTTATGCTTGTGGGTTTGGGAGGAAACAATGGATCAACTCTCACCGCTGGTGTGATTGCGAACAAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA