Sequence
atgc intronic sequence ATGC exonic sequencegtgattcaccttcttctacttcatatatatcttatctttacttagaaaccttgatcattaagattgatggtctgtctttcagCTTCAAATGGCGATCCCCGAACTCCAAGTTCTTTGCACTACATTGATCCATCAGGCAGATTAAACTCATATCAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08860.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0030g00570.t01 (Vitis vinifera), 3'ss of exon 11
gtgattcaccttc--ttctacttcatatatatcttatctttacttagaaaccttgat----cattaagattgatggtctgtctttcagCTTCAAATGGCGATCCCCGAACTCCAAGTTCTTTGCACTACATTGATCCATCAGGCAGATTAAACTCATATCAACAG
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gtaaatactcttcagctttgcaggattgctatctttttgcttttttgtaatttttctgtttcatgagcggccattttattttgtccagCTTCAAATGGAAATCCTCGAACTCCAGATTCTTTGCACTACATTGATCCTTCTGGCAGGTTCAATGCTTACCAACAG
upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0030g00600.t01 (Vitis vinifera), 3'ss of exon 8
gtgattcaccttc--ttctacttcatatatatcttatctt-tacttagaaaccttgatcattaagattgatggtctgtcttt---cagCTTCAAATGGCGATCCCCGAACTCCAAGTTCTTTGCACTACATTGATCCATCAGGCAGATTAAACTCATATCAACAG
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gtaaatactcttcagctttgcaggattgctatctttttgcgtttttataatttttctgtttcatgagcggccgttttattttgtccagCTTCAAATGGAAATCCTCGAACTCCAGATTCTTTGCACTACATTGATCCTTCTGGCCGGTTCAATGCTTACCAACAG
upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0030g00550.t01 (Vitis vinifera), 3'ss of exon 7
gtgattcaccttc--ttctacttcatatatatcttatctt-tacttagaaaccttgatcattaagattgatggtctgtcttt---cagCTTCAAATGGCGATCCCCGAACTCCAAGTTCTTTGCACTACATTGATCCATCAGGCAGATTAAACTCATATCAACAG
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gtaaatactcttcagctttgcaggattgctatctttttgcgtttttataatttttctgtttcatgagcggccattttattttgtccagCTTCAAATGGAAATCCTCGAACTCCAGATTCTTTGCACTACATTGATCCTTCTGGCAGGTTCAATGCTTACCAACAG
upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv12s0121g00080.t01 (Vitis vinifera), 3'ss of exon 10
gtgattcaccttc--ttctacttcatatatatcttatctt-tacttagaaaccttgatcattaagattgatggtctgtcttt---cagCTTCAAATGGCGATCCCCGAACTCCAAGTTCTTTGCACTACATTGATCCATCAGGCAGATTAAACTCATATCAACAG
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gtaaatactcttcagctttgcaggattgctatctttttgcgtttttataatttttctgtttcatgagcggccgttttattttgtccagCTTCAAATGGAAATCCTCGAAATCCAGATTCTTTGCACTACATTGATCCTTCTGGCCGGTTCAATGCTTACCAACAG
upper sequence: AT1G08860.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0030g00540.t01 (Vitis vinifera), 3'ss of exon 8
gtgattcaccttc--ttctacttcatatatatcttatctt-tacttagaaaccttgatcattaagattgatggtctgtcttt---cagCTTCAAATGGCGATCCCCGAACTCCAAGTTCTTTGCACTACATTGATCCATCAGGCAGATTAAACTCATATCAACAG
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gtaaatactcttcagctttgcaggattgctatctttttgcgtttttataatttttctgtttcatgagcagctgttttattttgtccagCATCAAATGGAAATCCGCGAACTCCAGATTCTTTGCACTACATTGATCCTTCTGGCCAGTTCAATGCTTACCAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcttatctttacttagaaaccttgatcattaagattgatggtctgtctttcagCTTCAAATGGCGATCCCCGAACTCCAAGTTCTTTGCACTACATTGATCCATCAGGCAGATTAAACTCATATCAACAG
gattgat putative branch site (score: 4)
tctgtctttc putative PPT
attaagatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattcaccttcttctacttcatatatatcttatctttacttagaaaccttgatcattaagattgatggtctgtctttcagCTTCAAATGGCGATCCCCGAACTCCAAGTTCTTTGCACTACATTGATCCATCAGGCAGATTAAACTCATATCAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT