Sequence
atgc intronic sequence ATGC exonic sequence...gcttaatagaagatccttggtctctcttcctttgaatacttagtatgttggcactaccccctatggttgttacttgttatttatttttctgattctgaagGTCGGAGGTCAAATCAGTCTTTATCGGGGAAGCAGCATTGTTTTCGGGTTATCAAAATATCCAATTTCAGAATTTGAGCTTGTTGCTGAAGAACTTTTAA
Basic information
| species | Arabidopsis thaliana |
| transcript | AT5G47020.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g10380.1 (Oryza sativa), 3'ss of exon 3
gcttaatagaagatccttggtctctcttcctttgaatacttagtatgttggcac-taccc-cctatg-gttgttacttgttatttatttttctgattctgaagGTCGGAGGTCAAATCAGTCTTTATCGGGGAAGCAGCATTGTTTTCGGGTTATCAAAATATCCAATTTCAGAATTTGAGCTTGTTGCTGAAGAACTTTTAA
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-tttgcgaggtgctgctttttattgtttcctgt-attaccatctccacttatgcgtacctgcctgtccactaatacattctctccttttttctatttatca-gGTCACAGGCCAAATTAGACTACTTAGCAAGGGTAGCATCAGCTTTGGGTTGTCTGAAAATCCAATATCAGAATTTGAGCTGGTTGCAGAAGAGCTTTTAA
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G385413_T01 (Zea mays), 3'ss of exon 3
-gcttaatagaagatccttggtctctcttcctttgaatacttagtatgttggcactaccccctatg-gttgttacttgttatttatttttctgattctgaagGTCGGAGGTCAAATCAGTCTTTATCGGGGAAGCAGCATTGTTTTCGGGTTATCAAAATATCCAATTTCAGAATTTGAGCTTGTTGCTGAAGAACTTTTAA
||| | ||||| | | | | || | | || | ||| || | | | | || |||||| ||| | | ||| ||||||||| || | | || || || ||||||||| || ||||||| |||||||||||||| |||||||||||||||||||
cgctatttttgagatcttatttaatacctgattgcagttatttatttgt-accattttctgtcgcatactagcatttccatcactattttctcattgtca-gGTGACAGGTCAAATTAGATTACTAACCAAGGGTAGTATCTGCTTTGGGTTATCAGAAAATCCAATATCAGAATTTGAGCTGGTTGCTGAAGAACTTTTAA
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G04290.1 (Glycine max), 3'ss of exon 3
-gcttaatagaagatccttggtctctcttcctttgaatacttagtatgttggcactacccccta-tggttgttacttgttatttatttttctgattctgaagGTCGGAGGTCAAATCAGTCTTTATCGGGGAAGCAGCATTGTTTTCGGGTTATCAAAATATCCAATTTCAGAATTTGAGCTTGTTGCTGAAGAACTTTTAA
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atttcattggtatattttatatttttctttattaatcattgcaatgtttaaccattggagccaaatgtttgatatttgtt--tgacttctttaattatgaagGTAAGAGGCCAAATTAGTGTATACAGTGGTGGAAGCTTAATCTTTGGGTTGTCTGATTATCCAATTTCTGAGTTTGAGCTTGTTGCAGAAGAGCTTTTAT
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G41140.1 (Glycine max), 3'ss of exon 3
gcttaatagaagatccttggtctctcttcctttgaatact-tagtatgttggcactacccccta-tggttgttacttgttatttatttttctgattctgaagGTCGGAGGTCAAATCAGTCTTTATCGGGGAAGCAGCATTGTTTTCGGGTTATCAAAATATCCAATTTCAGAATTTGAGCTTGTTGCTGAAGAACTTTTAA
|| || || || | | | || | | | | | | | || | || | || ||| || ||| | | | || ||| ||| ||||||| |||| ||||| ||| | || | ||| | ||| | | || ||||| || | ||||||||||| || |||||||||||||| ||||| ||||||
atttcattgatatattttatatttttctttattaatcattgcaatgtttaaccattggagccaaatgtttgatatttgct--taaattctctaattatgaagGTAAGAGGCCAAATTAGTGTATACAGTGGAGGAAGCTTAATCTTTGGGTTGTCTGATTATCCAATTTCTGAGTTTGAGCTTGTTGCAGAAGAGCTTTTAC
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 3
gcttaatagaagatccttg-gtctctcttcctttgaatacttagtatgttggcactaccccctatggttgttacttgttatt----tatttttctgattctgaagGTCGGAGGTCAAATCAGTCTTTATCGGGGAAGCAGCATTGTTTTCGGGTTATCAAAATATCCAATTTCAGAATTTGAGCTTGTTGCTGAAGAACTTTTAA
|||| | | | | | | | | ||||| || ||| | || | | | || | || || | | || | || | |||| || || | ||||| |||||||||| | || | || ||||||| | || || | ||| | |||||||| |||||||||||||||||||| ||||||||||| |
-----atagcaactattagaggcaatttacctttttgtatttattctgattttaatccctcttaaggatagtttttaatgttccattgattttttggttgtaaagGTGAGAGGTCAAATTAAACTACTCTGTGGGGGCAGCATCATCTTTGGACTGTCAGAGTATCCAATCTCAGAATTTGAGCTTGTTGCAGAAGAACTTTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttggcactaccccctatggttgttacttgttatttatttttctgattctgaagGTCGGAGGTCAAATCAGTCTTTATCGGGGAAGCAGCATTGTTTTCGGGTTATCAAAATATCCAATTTCAGAATTTGAGCTTGTTGCTGAAGAACTTTTAA
ttctgat putative branch site (score: 3)
tttttctg CT-rich tract
ttgttacttgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttaatagaagatccttggtctctcttcctttgaatacttagtatgttggcactaccccctatggttgttacttgttatttatttttctgattctgaagGTCGGAGGTCAAATCAGTCTTTATCGGGGAAGCAGCATTGTTTTCGGGTTATCAAAATATCCAATTTCAGAATTTGAGCTTGTTGCTGAAGAACTTTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - aatagaa
- - - - - - - - - - tctctct
- - - - - - - - - - - - - - - - - - - - - - - - - -cactacc
