Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatttgttgatgatttgatggaaaatgaaaaatctgtctcgttcctcaactaattgatatttgtaacattggtaactgtagATTAAGTAGGTGCACATCGATTACTACTGGTGAAGATGGTCCCATTCCAAGATGTAAACCTTTCAAGTATACATACGAAAAGGAGATTGTCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G44270.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 6
gtaagtatttgttgatgatttgatggaaaatgaaaaatctgtctcgttcctcaactaattgatatttgtaacattggtaactgtagATTAAGTAGGTGCACATCGATTACTACTGGTGAAGATGGTCCCATTCCAAGATGTAAACCTTTCAAGTATACATACGAAAAGGAGATTGTCAT
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----------gttagtg--ctgatcattcctttgtcctttttttgggtggttgat--gttaatgctgattttctttata--tatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATCCCAAGATGCAAGCCTTTCAAATACACCTACGAGAAGGAGATTGTTAT
upper sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G402242_T02 (Zea mays), 3'ss of exon 5
gtaagtatttgttg-atgatttgatgg----aaaatgaaaaatctgtctcgttcctcaactaattgatatttgtaacattggtaactgtagATTAAGTAGGTGCACATCGATTACTACTGGTGAAGATGGTCCCATTCCAAGATGTAAACCTTTCAAGTATACATACGAAAAGGAGATTGTCAT
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gtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatacttttggttgactttttatgacgtgttgctcctgca-ttatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAGATGCAAGCCCTTCAAGTATACCTATGAGAAGGAGATCGTTAT
upper sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 5
gtaa-gtatttgttgat--gatttgatggaaaatgaaaaatctgtctcgttcctcaa-ctaattgat-atttgtaacattggtaactgtagATTAAGTAGGTGCACATCGATTACTACTGGTGAAGATGGTCCCATTCCAAGATGTAAACCTTTCAAGTATACATACGAAAAGGAGATTGTCAT-------
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gtaatgcattgataggttaaactttctttttctttcaggcttcttctcgcttttctttctggctgctgagttgatgcatttact-ttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaaatctgtctcgttcctcaactaattgatatttgtaacattggtaactgtagATTAAGTAGGTGCACATCGATTACTACTGGTGAAGATGGTCCCATTCCAAGATGTAAACCTTTCAAGTATACATACGAAAAGGAGATTGTCAT
tggtaac putative branch site (score: 2)
taattgatatttgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatttgttgatgatttgatggaaaatgaaaaatctgtctcgttcctcaactaattgatatttgtaacattggtaactgtagATTAAGTAGGTGCACATCGATTACTACTGGTGAAGATGGTCCCATTCCAAGATGTAAACCTTTCAAGTATACATACGAAAAGGAGATTGTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT