Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaaatagacattagccagatatcatctttttatcattcatattgcattgagtgtactaatgacattttttataatgtaccagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGGGGATTTGCTGCAGATGTTGTTGCTGCTATAGACCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G20430.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G20430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G21920.1 (Glycine max), 3'ss of exon 4
--------------gtaagtaaatagacattagccagatatcatctttttatcattcatattgcattgagtgtactaatgacattttttataatgtaccagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGGGGATTTGCTGCAGATGTTGTTGCTGCTATAGACCAG
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gtctgattttgttttttaattatttcat-ttaaccttgtatagtttcctttttaaaaaaaaatagtaatttaagttagtgctgcatttcaatcttttacagCATTGCTGTTTACAAGGCATTATACAAGAGCTTTGGTGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
upper sequence: AT4G20430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 4
-------------gtaagtaaatagacattagccagatatcatctttttatcattcatattgcattgagt-gtactaatgacattttttataatgtaccagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGGGGATTTGCTGCAGATGTTGTTGCTGCTATAGACCAG
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cccatagaatgtgctatccccatag-tattaagtattcaacttcccatgacttttaaaagaaaaataatttatgcttgtgttgcatttcaatcttttacagCATTGCTGTTTACAAGGCACTATACAAAAGCTTTGGAGGATTTGCTGCAGATGTTGTTGCAGCTATTGACCAG
upper sequence: AT4G20430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G30460.1 (Glycine max), 3'ss of exon 4
------gtaag-taaatagacattagccagatatcatcttt-ttatcattcatattgcat---tgagtgtactaatgacattttttataatgtac--cagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGGGGATTTGCTGCAGATGTTGTTGCTGCTATAGACCAG
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tctgttctaacctggatttctaataattacatgcaagcataattaatttttattctatatatgtaaacatttgaatgcattccatttcaatcttttacagCATTGCCATTTACAAGGCACTATACAAGAGATTTGGAGGATTTGCAGCAGATGTTGTTGCAGCTATTGACCAG
upper sequence: AT4G20430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G13590.1 (Glycine max), 3'ss of exon 4
-------gtaag-taaatagacattagccagatatcatc-tttttatcattcatat--tgcattgagtgtactaatgacattttttataatgtac--cagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGGGGATTTGCTGCAGATGTTGTTGCTGCTATAGACCAG
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atctgttctaacctggatttctaataactacatgcaagcataattattttttattctatgtatgcaacatttgaatgcattccatttcaatcttttacagCATTGCCATTTACAAGGCACTATACAAGAGATTTGGAGGATTTGCAGCGGATGTTGTTGCAGCTATTGACCAG
upper sequence: AT4G20430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtaaatagacattagccagatatca------tctttttat---cattcatattgcattgagtgtactaatgac-----attttttataatgtaccagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGGGGATTTGCTGCAGATGTTGTTGCTGCTATAGACCAG
||| ||| | | || | | || || | |||||| || | ||| || | | || || || || ||| | | |||| ||| |||||||||||||| | || || ||||| || || ||||||||||||||||||||||| |||||||||
-taaagaaaaaaatatctgtctcatgtccatgtacccgttttataggcacatacattttttttctggcattaggcactaactatattctattcttttccagCATTGCTGTTTACAAGGCACTCTACAAAAGTTTCGGAGGCTTTGCTGCAGATGTTGTTGCTGCGATAGACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatcattcatattgcattgagtgtactaatgacattttttataatgtaccagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGGGGATTTGCTGCAGATGTTGTTGCTGCTATAGACCAG
tactaat putative branch site (score: 1)
tactaatgacattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaaatagacattagccagatatcatctttttatcattcatattgcattgagtgtactaatgacattttttataatgtaccagTATTTCTGTTTACAAGGCATTGTATAAGAGTTTTGGGGGATTTGCTGCAGATGTTGTTGCTGCTATAGACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT