Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcttgttaattttttttaataatatctcagaactgcttattcctctgcacattttgatttgtatgcttctttttgttctaacgaaaaattggcctttcagTCACACAGCAGCTATTGCAGCTGGGAACAATGGTATTCCAGTGAGGATGCACGGTTATGAGTTTGGAAAAGCAAGCGGGATGGCTCCTCGTGCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30020.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------------------------------gtttgtcttgttaattttttttaataatatctcagaactgcttattcctctgcacat-tttgatttgtatgcttctttttgttctaacgaaaaattggcctttcagTCACACAGCAGCTATTGCAGCTGGGAACAATGGTATTCCAGTGAGGATGCACGGTTATGAGTTTGGAAAAGCAAGCGGGATGGCTCCTCGTGCAAG
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gttagaccatgcttccttctttattaacttcttcacttggaagtaggattcttcagatgctctctttataaggggtgctgtgctcaaaataaaagaaaactgtttctatgtcttataaacataggaaatgggtagtaccaatttgataacggttgttctgttaacaattcccccattcttcttgc---atcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 3
gtttgtcttgttaattttttttaataatatctcagaactgcttattcctctgcacattttgatttgtatgcttctttttgttctaacgaaaaattggcctttcagTCACACAGCAGCTATTGCAGCTGGGAACAATGGTATTCCAGTGAGGATGCACGGTTATGAGTTTGGAAAAGCAAGCGGGATGGCTCCTCGTGCAAG
| | | | || | ||| | | | | | | ||| | | || ||| | | ||||||| | | || || |||||| ||||| ||||||||||||| | ||||| ||||| ||||||||||| || |||| ||||| |||||||| || |||||||| ||||| ||
--ctatttctatgtcttataaacataggaaatgggtagtaccaatttgataacgattgttcttttaacaattccccgttgttcttgc---atcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtcttgttaattttttttaataatatctcagaactgcttattcctctgcacattttgatttg-tatgcttctttt--tgttctaacgaaaaattggcctttcagTCACACAGCAGCTATTGCAGCTGGGAACAATGGTATTCCAGTGAGGATGCACGGTTATGAGTTTGGAAAAGCAAGCGGGATGGCTCCTCGTGCAAG
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--atgatagtttgattttcttt--taatattttgttcccattta---ctctgttttatttgattgggtctggttcatttgttgtttcttgggaatactggacaa-cagTCACACAGCAGCTATTGCAGCTGGAAATAATGGAATTCCAGTGAGAATGCATGGGTATGAATTTGGGAAAGCAAGTGGGATGGCTCCCCGTGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcacattttgatttgtatgcttctttttgttctaacgaaaaattggcctttcagTCACACAGCAGCTATTGCAGCTGGGAACAATGGTATTCCAGTGAGGATGCACGGTTATGAGTTTGGAAAAGCAAGCGGGATGGCTCCTCGTGCAAG
ttctaac putative branch site (score: 1)
cctttc putative PPT
attttgatttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcttgttaattttttttaataatatctcagaactgcttattcctctgcacattttgatttgtatgcttctttttgttctaacgaaaaattggcctttcagTCACACAGCAGCTATTGCAGCTGGGAACAATGGTATTCCAGTGAGGATGCACGGTTATGAGTTTGGAAAAGCAAGCGGGATGGCTCCTCGTGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC