Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtcctttagatgtgtttttttatcattctgctgatacttgaagagcctaaacattgtttttattattttcttgcagATCTTATCAGATGATGAGAAAAGATCTCTATACGACAGATATGGCGAGGCAGGAGTTAAAGGCGCTGGAATGGGAGGCATGGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39960.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G31080.1 (Glycine max), 3'ss of exon 6
gtaaagtcct---ttagatgtgtttttttatcattctgctgatacttgaagagcctaaacattgtttttattattttc-ttgcagATCTTATCAGATGATGAGAAAAGATCTCTATACGACAGATATGGCGAGGCAGGAGTTAAAGGCGCTGGAATGGGAGGCATGGGG
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gtaaaactgcagattattaaactcagtttgcccttatgcatatgtttaacaataacttgtcttctgcgaataaattccattgcagGTGTTATCAGATGATGAGAAACGATCCATATATGACAGATTTGGAGAGGCTGGGCTTAAAGGTTCTGGAATGGGG---ATGGGG
upper sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G01960.1 (Glycine max), 3'ss of exon 6
------gtaaagtcctttagatgtgtttttttatcattc-tgctgatacttgaagagcctaaacattgtttttattattttcttgcagATCTTATCAGATGATGAGAAAAGATCTCTATACGACAGATATGGCGAGGCAGGAGTTAAAGGCGCTGGAATGGGAGGCATGGGG
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gtaaatctacagcttgttgaacacagctggccattatgcatgtctactcgtaattgatctt----ctgtaattcaaattcttttgcagGTCTTGTCAGATGATGAGAAACGATCCATATATGACACATATGGAGAGGCTGGACTTAAGGGTTCAGGAATGGG---CATGGGG
upper sequence: AT4G39960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0324g00040.t01 (Vitis vinifera), 3'ss of exon 9
gtaaa-gtcctttagat--gtgtttt---tttatcattctg-ctgatacttgaagagcctaaacattgtttttattattttcttgcagATCTTATCAGATGATGAGAAAAGATCTCTATACGACAGATATGGCGAGGCAGGAGTTAAAGGCGCTGGAATGGGAGGCATGGGG
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gtaaaagttcttttgattcatgatttagcttcaacagtttgattgctatctataaaacaattggtttattggcaagctacttgtgcagGTTTTGTCAGATGATGAGAAAAGATCCTTATACGACAGGTATGGGGAAGCAGGACTTAAAGGTGCTGGTATGGG---CATGGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcattctgctgatacttgaagagcctaaacattgtttttattattttcttgcagATCTTATCAGATGATGAGAAAAGATCTCTATACGACAGATATGGCGAGGCAGGAGTTAAAGGCGCTGGAATGGGAGGCATGGGG
gcctaaa putative branch site (score: 3)
tttttattattttctt putative PPT
taaacattgtttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtcctttagatgtgtttttttatcattctgctgatacttgaagagcctaaacattgtttttattattttcttgcagATCTTATCAGATGATGAGAAAAGATCTCTATACGACAGATATGGCGAGGCAGGAGTTAAAGGCGCTGGAATGGGAGGCATGGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA