Sequence
atgc intronic sequence ATGC exonic sequencegtcagtatgctgctacaacctgtctgtttcaatgttgacaggcgttatgctgatgctttattatcttgcttggatttcagGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G63700.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g47240.3 (Oryza sativa), 3'ss of exon 8
--------gtcagtatgctgctacaacctgtctgtttca-----atgttgacaggcgttatgctgatgctttattatcttgcttggatttcagGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGT
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gtatcactgaaaatctttacttgttaattttttgtttcatgcatatcttattgccatttctgtacatcacatactatgcaacacatacg-cagGTTATAAAAAACTCAAATGGGTGCAACCTAGCTGTTGACATATGGAGTTTGGGATGCACTGTCCTGGAGATGGCTACATCGAAACCGCCATGGAGCCAGT
upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------gtcagt--atgctgctacaacc-tgtctgtttcaatgttgacaggcgttatgctgatgctttattatct-tgcttggatttcagGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGT
|| | | ||| || | | | | | |||| | | || | || | | | | | | ||||| ||||| ||||| ||||| |||| ||||| || ||||||||||| | ||||| || |||||||| |||||||| | ||||| ||||||||||| |
gtaatgaaaatcctacattcttctacacttctctagttatttgatgaatttatgcctatcttctctccgctGTTATAAAAATCAACCTTGCTTCTCTCACACATGTAATAACTATGCAGGTTATAAAAAATTCTAATGGATGTAATCTTGCTGTTGACATATGGAGCTTAGGATGCACGGTTTTAGAGATGGCTACCTCAAAACCACCATGGAGCCAAT
upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 7
gtcagtatg-ctgctacaacctgtctgtttcaatgttgacaggcgttatgc---tgatgctttattatctt-------gcttggatttca--gGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGT
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gtcagaatgatttctacatccattcaacactttttgttgcagatgctttgtctgtagtatattcttatctttgtcactgcctcaattacatagGTTATAAAAAATTCAAATGGTTGTAATCTTGCGGTTGATATATGGAGTCTAGGATGCACTGTTTTGGAGATGGCAACAACAAAACCTCCTTGGAGCCAAT
upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 7
gtcagtatg----ctgctacaacctgt-ctgtttcaatgttgacaggcgttatgctg-atgctttattatcttgcttggatt--tcagGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGT
||||||||| || ||| || | ||| | |||| | || || ||| | ||||| |||| |||||||||| ||||||||||| |||| ||||| || || |||||||| ||||| | ||| ||||| || |||||||| || |||||||| |||||||| |
gtcagtatgatttctttgttaacttgcatttttttgttattgatgcttttgatataatattgtttgtgtcactgctttgattgtctagGTGATAAAAAATTCAAATGGTTGTAATCTTGCTGTTGATATATGGAGCCTTGGCTCTACCGTTTTTGAGATGGCTACTACAAAACCTCCTTGGAGCCAAT
upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 10
gtcagtatg-ctgctacaacctgtctgtttcaatgttgacaggcgttatgctgatgctttattatcttgcttggatt--tcagGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGT
||||||||| | || || | || ||| | | | | | || ||| | || || |||| |||||||||||||||||||||| |||| ||||| || || |||||||| ||||| | || ||||| || |||||||| || |||||||| |||||||| |
gtcagtatgatttctttgttgagttttttgtaattgatgcttttgatgtaatattg-tttgtgtcactgttttgattgtctagGTGATAAAGAATTCAAATGGTTGTAATCTTGCTGTTGATATATGGAGCCTTGGCTCCACCGTTTTCGAGATGGCTACTACAAAACCTCCTTGGAGCCAAT
upper sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 9
gtcagtatgctgctacaacctgt-ctgtt--tcaatgtt---gacaggcgtta-tgctgatgctttattatcttgcttggatttcagGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGT
||||| || | | ||| ||||| ||| |||| |||| | || | | | || | || || ||||||| |||||||| ||||||||| |||| ||||| ||||| ||||||||||||| || || ||||| || ||||||||||| ||||| || ||||||||||
gtcagcctggttttcatttttgtactgttggtcactgttcttgacaatcctttctagtaacatatt-tgattgaatttatcattcagGTCATAAAGAACTCAAATGGCTGTAATCTTGCAGTCGATTTATGGAGTCTTGGGTGCACAGTTTTGGAGATGGCTACAACAAAACCACCTTGGAGCCAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttcaatgttgacaggcgttatgctgatgctttattatcttgcttggatttcagGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGT
tgctgat putative branch site (score: 3)
tcttgctt putative PPT
tttattatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtatgctgctacaacctgtctgtttcaatgttgacaggcgttatgctgatgctttattatcttgcttggatttcagGTGATAAAGAATTCAAATGGCAGTAACCTTGCGGTCGACATATGGAGTCTTGGATGTACTGTTTTAGAAATGGCTACAACGAAACCTCCATGGAGCCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA