Sequence
atgc intronic sequence ATGC exonic sequence...gtggaatttgttgttcatgtattgcttgaacggccatgctcgttaatatactaaacccatcagacacgagatcatgacagttctgagtatgaatttacagGAGGTACATGGGTCACAAGAGGACCATCAGGCCAAATGCAAAGAAGCTCAGTGCATTGTTCATGGACCGGGAAAAGATGGAGTGGCAAACTTTCGCCAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16650.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 8
-----------------gtggaa----tttgttgttcatgtattgcttgaacggccatgctcgttaatatactaaacccatcagacacgagatcatgacagttctgagtatgaatttacagGAGGTACATGGGTCACAAGAGGACCATCAGGCCAAATGCAAAGAAGCTCAGTGCATTGTTCATGGACCGGGAAAAGATGGAGTGGCAAACTTTCGCCAAA
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gtaagaatgaatacatgatgccatcctttaattcttcctttatgtttcaaaaaatgatatacgat--taacctgttttcctttgactatcaacctt--ctgttctgattgtacaaa-acagGAGGTATATGGGTCACAAAAGAACCATCAGACCAAATGCAAAGAAGCTTAGTGCGCTGTTCATGTCAAGGCATGAGATGGACTGGGATACATTTGCAAGT
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G15170.1 (Glycine max), 3'ss of exon 8
-----gtggaatttgttgt-tcatgtattgcttgaacggccatgctc-----gttaatatactaaacccatcagacacgagatcatgacagttctgagtatgaatttacagGAGGTACATGGGTCACAAGAGGACCATCAGGCCAAATGCAAAGAAGCTCAGTGCATTGTTCATGGACCGGGAAAAGATGGAGTGGCAAACTTTCGCCAAA
|||| | || |||| || || | ||| | || ||| | || | | || | || | | |||| | | | |||||||||| ||||||||||| || |||||||| ||||||||||||||||| ||||| |||||||| || | ||||||| ||| | || || || |
gtaataatgaatgcatggtgtcatccttttattcttcctttatgtttaaaaaatttatacgattaatgtgtttggcatct-actataaacctgctgattgtacaaa-acagGAGGTATATGGGTCACAAAAGAACCATCAGACCAAATGCAAAGAAGCTTAGTGCGCTGTTCATGTCAAGGCATGAGATGGACTGGGATACATTTGCAAGT
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G03640.1 (Glycine max), 3'ss of exon 9
-gtggaatttgttgttcatgtattgcttgaacggccatgctcgttaatatactaaacccatcagacacgagatcatgacagttctgagtatgaattt--acagGAGGTACATGGGTCACAAGAGGACCATCAGGCCAAATGCAAAGAAGCTCAGTGCATTGTTCATGGACCGGGAAAAGATGGAGTGGCAAACTTTCGCCAAA
||| | || | | | | || || | | || || | || || | | | || || | | | | || | ||||| || ||||||||||| || || ||||| ||||||||||||||||| || | | || || || | | ||||| ||| | || || ||||||
tgtgcataatgct-tgcttttactgactaacatattatcttcctattcat-ttatttttggctaatgtgcc-tcctgttaacctttcattttgtttacaatagGAGATATATGGGTCACAAAAGAACAATCAGACCAAATGCAAAGAAGCTTAGCACGCTATTGGCGGGAAGGCATCAAATGGACTGGGATACCTTTGCCAAA
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv00s0229g00100.t01 (Vitis vinifera), 3'ss of exon 8
-----gtggaatttgttgttcatgtattgcttgaacggccatgctcgttaatatactaaacccatcagacacgagatcatgacagttctgagtatgaatttacagGAGGTACATGGGTCACAAGAGGACCATCAGGCCAAATGCAAAGAAGCTCAGTGCATTGTTCATGGACCGGGAAAAGATGGAGTGGCAAACTTTCGCCAAA
|||| || |||||||| ||| | | | || ||| || | || | ||| | |||| ||| ||| | |||||||||||||| || |||||||||||||||||||||||||| ||||||||||| |||||||||| ||| | |||||||| ||| | || || |||||
tatttttggacatttctgttcatgatatgcaccctttttcttctttcttttgggactgttccactt---cattaaatcg-gtttattcttgctattgatt-aaagGAGGTACATGGGGCATAAGAGGACCATCAGGCCAAATGCAAAAAAGCTCAGTGCTTTGTTCATGGCTCGGAATAAGATGGACTGGGATACATTTGCCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatactaaacccatcagacacgagatcatgacagttctgagtatgaatttacagGAGGTACATGGGTCACAAGAGGACCATCAGGCCAAATGCAAAGAAGCTCAGTGCATTGTTCATGGACCGGGAAAAGATGGAGTGGCAAACTTTCGCCAAA
tactaaa putative branch site (score: 1)
tatgaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggaatttgttgttcatgtattgcttgaacggccatgctcgttaatatactaaacccatcagacacgagatcatgacagttctgagtatgaatttacagGAGGTACATGGGTCACAAGAGGACCATCAGGCCAAATGCAAAGAAGCTCAGTGCATTGTTCATGGACCGGGAAAAGATGGAGTGGCAAACTTTCGCCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - ctaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagacac