Sequence
atgc intronic sequence ATGC exonic sequence...atttgttcaattgcaaagattaggattaggaagaaattggtttagagtatattctggaatcgtcttgtttgttcattggtgttttacgctgatgatacagGAGATTTCTTGCTATTTGGGTCTGGACCTTGGGAAAATCAAGATTAAACGCTTTGCTGATGGTGAGATCTATGTTCAGCTACAAGAGAGTGTAAGGGGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G44530.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G44530.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 3'ss of exon 2
atttgttcaattgcaaag-attaggattaggaagaaattggtttagagtatattctggaatcgtcttgtttgttcattggtgttttacgctgat---gatacagGAGATTTCTTGCTATTTGGGTCTGGACCTTGGGAAAATCAAGATTAAACGCTTTGCTGATGGTGAGATCTATGTTCAGCTACAAGAGAGTGTAAGGGGAT
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----atttaagtgtgacttgttacaagtagcacttgtttgactgaatggttaatctcacagtgccaaactaagatggaagtttttcttgttgtcttatctgcagGAAATAGCAAGTTACTTGGGCTTAGAACTTGGGAAGATTAACATAAAAAGGTTTGCTGATGGCGAAATATATGTTCAGTTACAAGAAAGCGTAAGGGGAT
upper sequence: AT2G44530.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G24280.2 (Glycine max), 3'ss of exon 2
-atttg-ttcaattgcaaagattaggattaggaagaaattggtttagagt--atattctggaatcgtcttgtttgttcattggtgttttacgctgatgatacagGAGATTTCTTGCTATTTGGGTCTGGACCTTGGGAAAATCAAGATTAAACGCTTTGCTGATGGTGAGATCTATGTTCAGCTACAAGAGAGTGTAAGGGGAT
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aatatacttttgttgttta--ttaatatttgaagtcttatgttatacaccagatagtctctaattatttc-tgaaatgtttgattttgcatg-tatttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAATTAAGATAAAGCGTTTTGCTGATGGTGAGATATATGTCCAGCTGCAAGAGAGTGTCAGGGGGT
upper sequence: AT2G44530.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G12660.1 (Glycine max), 3'ss of exon 2
atttgttcaattgcaaagattaggattaggaagaaattggtttagagt--atattctggaatcgtcttgtttgttcattggtgttttacgctgatgatacagGAGATTTCTTGCTATTTGGGTCTGGACCTTGGGAAAATCAAGATTAAACGCTTTGCTGATGGTGAGATCTATGTTCAGCTACAAGAGAGTGTAAGGGGAT
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ttgaatatacttttatttattaatatttgaagtcttatgttatacagtagatagtctttaattatttactgaaatgtttgat-ttgcatg-tatttaagtagGAAATTGCATGCTACCTGGGCCTGGAGCTAGGAAAAACTAAGATAAAGCGTTTTGCTGATGGTGAGATATATGTCCAGCTGCAAGAGAGTGTCAGGGGGT
upper sequence: AT2G44530.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 3'ss of exon 2
atttgttcaattgcaaagattaggattaggaagaaattggtttagagtatattctggaatcgtcttgtttgt-tcattggtgttttacgctgatgat----acagGAGATTTCTTGCTATTTGGGTCTGGACCTTGGGAAAATCAAGATTAAACGCTTTGCTGATGGTGAGATCTATGTTCAGCTACAAGAGAGTGTAAGGGGAT
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-----actttttgtgcatgtttttttttttttttttttcatacaagtgtttctcccatgaccttttgtatgtgtcattcctgatgcataattatgtttgttgtagGAAATTGCATGCTACATGGGCCTGGAGCTGGGAAAAATAAACATAAAACGCTTTGCTGATGGAGAGATTTATGTTCAGTTGCAAGAGAGTGTTAGAGGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatattctggaatcgtcttgtttgttcattggtgttttacgctgatgatacagGAGATTTCTTGCTATTTGGGTCTGGACCTTGGGAAAATCAAGATTAAACGCTTTGCTGATGGTGAGATCTATGTTCAGCTACAAGAGAGTGTAAGGGGAT
cgctgat putative branch site (score: 4)
tgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgttcaattgcaaagattaggattaggaagaaattggtttagagtatattctggaatcgtcttgtttgttcattggtgttttacgctgatgatacagGAGATTTCTTGCTATTTGGGTCTGGACCTTGGGAAAATCAAGATTAAACGCTTTGCTGATGGTGAGATCTATGTTCAGCTACAAGAGAGTGTAAGGGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA