Sequence
atgc intronic sequence ATGC exonic sequence...acaatttggtgtaagattataaaagtgaaatcatcaaatccgatgtgattgatgatcagatcaacatatgcttaacttaagtacatcttgtcccaagtagGAGTAAGCAAGGACGGGCAAGTACGGCACTTCTTCCACCGGCCATCAAAGGCTTATACGACCGGAACACGAAAACGAAGAAAAGTGAGCACAGATGAGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G28470.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G28470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC201894.4_FGT007 (Zea mays), 3'ss of exon 2
acaatttggtgtaagattataaaagtgaaatcatcaaatccgatgtgattgatgatcagatcaacatatgcttaacttaagtacatcttgtcccaagtagGAGTAAGCAAGGACGGGCAAGTACGGCACTTCTTCCACCGGCCATCAAAGGCTTATACGACCGGAACACGAAAACGAAGAAAAGTGAGCACAGATGAGGA
| ||| | || | | ||| ||| | ||| || || || | ||| | | || || | || ||| || ||||||||||||| || |||||||||||||||||||| || | ||| || ||||| || || | || || | || ||| || | || ||
gtacgcacccgtagcttaattttcgctggtt--tcagatctg-cgtgcgtg-catccatatatatgcatgat-gatctaccgacgttgtgctggtttcagGTGTGAGCAAGGACGGGCTTGTCCGGCACTTCTTCCACCGGCCGTCCAGGGCGTACACGACGGGGACGAGGAAGCGGCGGAAGGTGCACAGCGGCGACGA
upper sequence: AT1G28470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G031200_T02 (Zea mays), 3'ss of exon 2
--aca-atttggtgtaagattataaaagtgaaatcatcaaatccgatgtgattg-atgatcagatcaacatatgcttaacttaagtacatcttgtcccaagtagGAGTAAGCAAGGACGGGCAAGTACGGCACTTCTTCCACCGGCCATCAAAGGCTTATACGACCGGAACACGAAAACGAAGAAAAGTGAGCACAGATGAGGA
|| | ||| | | || | | | || ||| || || || || | ||| | | || | || | | ||| || ||||||||||||| || |||||||||||||||||||| || | ||| || ||||| || || | || || | || ||| || | || ||
gtacgtacgcaccgtacgtagcttaattttcgctggtt---tcggatctgcgtgcgtgcatccatgcatgcatgatgatctaccgacgatgtgctggttttcagGTGTGAGCAAGGACGGGCTTGTTCGGCACTTCTTCCACCGGCCGTCCAGGGCGTACACGACGGGGACGAGGAAGCGGCGGAAGGTGCACAGCGGCGACGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattgatgatcagatcaacatatgcttaacttaagtacatcttgtcccaagtagGAGTAAGCAAGGACGGGCAAGTACGGCACTTCTTCCACCGGCCATCAAAGGCTTATACGACCGGAACACGAAAACGAAGAAAAGTGAGCACAGATGAGGA
gcttaac putative branch site (score: 3)
tcttgtccc putative PPT
ttaacttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaatttggtgtaagattataaaagtgaaatcatcaaatccgatgtgattgatgatcagatcaacatatgcttaacttaagtacatcttgtcccaagtagGAGTAAGCAAGGACGGGCAAGTACGGCACTTCTTCCACCGGCCATCAAAGGCTTATACGACCGGAACACGAAAACGAAGAAAAGTGAGCACAGATGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- aatttgg
- - - - - - - - - ataaaag
- - - - - - - - - - - - - - - -catcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacttaa