Sequence
atgc intronic sequence ATGC exonic sequencegtatcaacctttatgtctctgtctttgaaatgagttttttttctttctgtgattttgatttgaatgcgtatctttgtgtgtgatcttaagATGGACAATAGATGTTACCGGAGCTCCAGGGACACTTTACGCTAATGAGACTTATCAGCTTCAGGTTGAATTTCCTGAACATTACCCTATGGAAGCACCC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G45050.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G07810.1 (Glycine max), 3'ss of exon 2
gtatca-acctttatgtctctgtctttgaaatgagttttttttctttctgtgatt-ttgatttgaatgcgtat-ctttgtgtgtgatcttaagATGGACAATAGATGTTACCGGAGCTCCAGGGACACTTTACGCTAATGAGACTTATCAGCTTCAGGTTGAATTTCCTGAACATTACCCTATGGAAGCACCC
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gtaccagattcttctcaatccacaccctaaatattatcgatttcgttcttccattattcctttacattcctttgctttgtttctctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAATGAGACCTACCAGCTTCAGGTTGATTTTCCTGAGAATTACCCAATGGAGGCTCCT
upper sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 2
----------------------gtatcaacctttatgtctc-tgtctttgaaatgagtttttt-ttctttctgtgattttgatttgaatgcgtat-ctttgtgtgtgatcttaagATGGACAATAGATGTTACCGGAGCTCCAGGGACACTTTACGCTAATGAGACTTATCAGCTTCAGGTTGAATTTCCTGAACATTACCCTATGGAAGCACCC
| |||| | | | | | || | | || || || | | | ||| ||| | | | | |||||| | | ||| ||| | || || || |||||||| ||||||||||||||||| ||||| || ||||||||||| || |||||||| ||||||| |||||||| ||
gtaccagattcttctaattcccctctcaatcaacaccctaaatattctcgatttccttcttccattgttccctttacattgttttttgttcctttgctttgtttctctctggaagGTGGGTGGTTGAAGTCACTGGAGCTCCTGGGACACTTTACGCTAACGAGACCTACCAGCTTCAGGTCGATTTTCCTGAGAATTACCCGATGGAAGCTCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttctttctgtgattttgatttgaatgcgtatctttgtgtgtgatcttaagATGGACAATAGATGTTACCGGAGCTCCAGGGACACTTTACGCTAATGAGACTTATCAGCTTCAGGTTGAATTTCCTGAACATTACCCTATGGAAGCACCC
ttttgat putative branch site (score: 4)
attttgatttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcaacctttatgtctctgtctttgaaatgagttttttttctttctgtgattttgatttgaatgcgtatctttgtgtgtgatcttaagATGGACAATAGATGTTACCGGAGCTCCAGGGACACTTTACGCTAATGAGACTTATCAGCTTCAGGTTGAATTTCCTGAACATTACCCTATGGAAGCACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG