Sequence
atgc intronic sequence ATGC exonic sequencegtgagcttttctcttcgatttaagattaaaagtatgatcatttatgttatatcagattttcgtgttatttgtggtattcattgcttggatctgtattatgctttcgttgactagATTGATGTTGAGAATCCCTGTGTGATAATGAGTCAAGACAAGAGCAGGGAGTTCTTACATTCTGGTAACGACAAAGATAAATTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G07660.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G07660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G025340_T02 (Zea mays), 3'ss of exon 4
gtgagcttttctcttcgatttaagattaaaagtatgatcatttatgttatatcagattttcgtgttatttgtggtattcattgct-tggatctgtattatgctttcgttgactagATTGATGTTGAGAATCCCTGTGTGATAATGAGTCAAGACAAGAGCAGGGAGTTCTTACATTCTGGTAACGACAAAGATAAATTCAAG
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------aattgttttaatctttatcctttctgctggattacttatttgtaatgtgattgcca-gatatatgttgtctgcattctgatgcatctgtgtgacttttc--------agATTGAAGTTGAAAACCCTTGTGTAATTATGAGTCAAGACAAAAGCAGAGAGTTTTTACATTCAGGAAATGACAAGGATAAGTTCAAG
upper sequence: AT5G07660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0013g00490.t01 (Vitis vinifera), 3'ss of exon 4
--gtgagcttttctcttcgatttaagattaaaagtatgatcatttatgttatatcagattttcgtgttatttgtggtattcattgcttggatctgtattatgctttcgttgactagATTGATGTTGAGAATCCCTGTGTGATAATGAGTCAAGACAAGAGCAGGGAGTTCTTACATTCTGGTAACGACAAAGATAAATTCAAG
||| |||| | ||| | | | | | |||||| | | | | | | | | || | || || ||| ||| ||| || ||||||||||||| ||||| ||||||||||||||||||||||| ||||| || || || ||||| || || ||||||||||||||||||
taatgaaggattctata-aattctccttccccaattagtttatttattcaactttaaacatcctgctca---gtaatgtt------ttagatgtgtcttacttttct------cagATTGATGTTGAAAATCCATGTGTGATAATGAGTCAAGACAAAAGCAGAGAATTTTTGCATTCAGGGAATGACAAAGATAAATTCAAG
upper sequence: AT5G07660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ36741 (Selaginella moellendorffii), 3'ss of exon 4
gtgagcttttctcttcgatttaagattaaaagtatgatcatttatgttatatcagattttcgtgttatttgtggtattcattgcttggatctgtattatgctttcgttgactagATTGATGTTGAGAATCCCTGTGTGATAATGAGTCAAGACAAGAGCAGGGAGTTCTTACATTCTGGTAACGACAAAGATAAATTCAAG
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--------------------------------------------------gtgagtcttccgtaatatttttcctgtttactgacttgg--------atgctta-------tagATAGATGTCGAAAATCCTTGTGTGATCATGAGCCAAGACAAGAGCCGCGAGTTCCTGCATTCCGGAAATGACAAGGAAAAGTTTAAG
upper sequence: AT5G07660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ27923 (Selaginella moellendorffii), 3'ss of exon 4
gtgagcttttctcttcgatttaagattaaaagtatgatcatttatgttatatcagattttcgtgttatttgtggtattcattgcttggatctgtattatgctttcgttgactagATTGATGTTGAGAATCCCTGTGTGATAATGAGTCAAGACAAGAGCAGGGAGTTCTTACATTCTGGTAACGACAAAGATAAATTCAAG
| || || ||| ||||| | || | || | | |||||| ||||| ||||| || ||||| |||||||| ||||| |||||||||||| | |||||| | ||||| || || ||||| || || ||||||
--------------------------------------------------gtgagtcttccgtaatattttacctgtttactgacttgg--------atgctta-------tagATAGATGTCGAAAATCCTTGTGTGATCATGAGCCAAGACAAGAGCCGCGAGTTCCTGCATTCCGGAAATGACAAGGAAAAGTTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgtgttatttgtggtattcattgcttggatctgtattatgctttcgttgactagATTGATGTTGAGAATCCCTGTGTGATAATGAGTCAAGACAAGAGCAGGGAGTTCTTACATTCTGGTAACGACAAAGATAAATTCAAG
ctttcgtt CT-rich tract
ttatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcttttctcttcgatttaagattaaaagtatgatcatttatgttatatcagattttcgtgttatttgtggtattcattgcttggatctgtattatgctttcgttgactagATTGATGTTGAGAATCCCTGTGTGATAATGAGTCAAGACAAGAGCAGGGAGTTCTTACATTCTGGTAACGACAAAGATAAATTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG