Sequence
atgc intronic sequence ATGC exonic sequencegttagttgaagtttatttttctccttaagattccattatggtagctccgtggtggcaactctagtgccatgtggctgaattctatttttttaattctattttcagGATATTCAAGAGGCACATGCTGGACAAATCGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G45332.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 9
---------------------------gttagttg--aagtttatttttctccttaagattccattatggtagctccgtggtg-gcaactctagtgccatgtggctgaattctatttttttaattctattttcagGATATTCAAGAGGCACATGCTGGACAAATCGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
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gtaagttgcaccagatgttgtaaccaaaataattactaagtattagtttgatctgatcattggagttgattgtttcctttataagcaaatccacccctaggctaatatcttctttattctgtggtcaatat--agGATATTCAAGAAGCACATGCTGGTCAAATTGTTGCTGTCTTTGGTGTTGATTGTGCGTCAG
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G056393_T01 (Zea mays), 3'ss of exon 9
gttagttgaagtttatttttctccttaagattccattatggtagctccgtggtggcaactctagtgccatgtggctgaattctatttttttaattctatt---ttcagGATATTCAAGAGGCACATGCTGGACAAATCGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
|| ||||| | | |||| | | || | || | ||| | || |||| | | | | | | ||| | | ||| | || | ||||||||||||| ||| ||||||| ||||| || ||||| |||||| |||| ||||||||||
gtaagttgcattagatttagttttcactcaatcagtattgat--ttccatcagatgaagatcagtgattttttgggtattaatgtttatattattttgtttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 9
gttagttgaagtttatttttctccttaaga-ttccattatggtagctccgtggtggcaactctagtgccatgtggctgaattctatttttttaattctattttcagGATATTCAAGAGGCACATGCTGGACAAATCGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
|| || | || | | || |||| || | ||| | | | || | | | | | | | | |||| || | | | | || | ||||| ||||||||||| |||||||| ||||| || ||||| |||||| | || ||||||||||
tttgtttcttgactaaatacattctgaagaatttgaatatattcagttattctctgccattttcttacaactt---ttaattgggttctctca---caatctgcagGACATTCAAGAGGCTCATGCTGGGCAAATAGTTGCTGTATTTGGTGTCGACTGTGCATCAG
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 4
gttagttgaagtttatttttctccttaaga-ttccattatggtagctccgtggtggcaactctagtgccatgtggctgaattctatttttttaattctattttcagGATATTCAAGAGGCACATGCTGGACAAATCGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
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tttgtttcttgactaaatacattctgaagaatttgaatatattcagttattgtctgccattttcttacaattt---ctaattgggttctctca---caatctgtagGACATTCAAGAGGCTCATGCTGGGCAAATAGTTGCTGTATTTGGTGTCGAATGTGCATCAG
upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S20_94V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------gttagttgaagtt----tatttttc--tccttaagattccattatggtagctccgtggtggca-actctagt----gccatgtggctgaattctatttttttaattctattttcagGATATTCAAGAGGCACATGCTGGACAAATCGTAGCTGTGTTTGGTATTGAGTGTGCATCAG---------------------------------------
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gttagtctgaatctctctccttgtccttttttttgtttctgttttgtttttgtgggttggtgtatcttttgaaagaatgatcaaacttatgctgcttttaggtttctaaagttgtgttgctggcgtgctgttgtgctacaccgtagttattatcatgtctct-acttacattctgcggagttgtatttcagGACATTCAAGAGGCACATGCTGGAGAAATTGTTGCAGTCTTTGGTGTTGAGTGTTCTTCTGGTGATACTTTTACGGACGGATCTGTGAAGTTTACGATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtggcaactctagtgccatgtggctgaattctatttttttaattctattttcagGATATTCAAGAGGCACATGCTGGACAAATCGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
ttttaat putative branch site (score: 3)
ttctattttc CT-rich tract
tgaattctattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttgaagtttatttttctccttaagattccattatggtagctccgtggtggcaactctagtgccatgtggctgaattctatttttttaattctattttcagGATATTCAAGAGGCACATGCTGGACAAATCGTAGCTGTGTTTGGTATTGAGTGTGCATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA