Sequence
atgc intronic sequence ATGC exonic sequence...cgttgaaaaataagattttacatatatataattatatatatatatatatatatatgtcacactttcttttgatatacatttggaattacattttgtgtagTTTGCTTGGACGGAAGCTTACCGGCGTATCATTTAGACAGAGGGTTTGGTGCTGGATCAAACAATTGGATTTTGCAGTTTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G23870.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G23870.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G29930.2 (Glycine max), 3'ss of exon 1
cgttgaaaaataagattttacatatatataattatatatatatatatatatatatgtcacactttcttttgatatacatttgg--aattacattt--tgtgtagTTTGCTTGGACGGAAGCTTACCGGCGTATCATTTAGACAGAGGGTTTGGTGCTGGATCAAACAATTGGATTTTGCAGTTTGAG
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-------------------gtaagttcatgataattaattaatttgtat-tat-tatcattattattatttattaaaatttggagaatcggaattatcttgtagTTTGTTTGGACGGAAGTTTACCGGCGTATCACTTGCACAGAGGATTTGGAGCTGGTAAAGACAACTGGCTTCTACAATTTGAG
upper sequence: AT5G23870.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0050g00570.t01 (Vitis vinifera), 3'ss of exon 1
----------------cgttgaaaaataagattttacatatatataattatatatatatatatatatatatgtcacactttcttttgatatacatttggaattacattttgtgtagTTTGCTTGGACGGAAGCTTACCGGCGTATCATTTAGACAGAGGGTTTGGTGCTGGATCAAACAATTGGATTTTGCAGTTTGAG
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gtgagtcatgagtcacgggtggagattaa--ttttatgtttattttatttttattctgttgatgagtgattgattttcctgttgcctttttcttttcggggaatgtttgtgtgtagTTTGCTTAGACGGGAGCTTGCCGGCGTATCATCTGCATAAAGGATTCGGAGCTGGAGCTACCAACTGGCTTTTGCAGTTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatatatatgtcacactttcttttgatatacatttggaattacattttgtgtagTTTGCTTGGACGGAAGCTTACCGGCGTATCATTTAGACAGAGGGTTTGGTGCTGGATCAAACAATTGGATTTTGCAGTTTGAG
ttttgat putative branch site (score: 4)
ttttgatatacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgttgaaaaataagattttacatatatataattatatatatatatatatatatatgtcacactttcttttgatatacatttggaattacattttgtgtagTTTGCTTGGACGGAAGCTTACCGGCGTATCATTTAGACAGAGGGTTTGGTGCTGGATCAAACAATTGGATTTTGCAGTTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA