Sequence
atgc intronic sequence ATGC exonic sequencegtcatatgtctagttttgctcacccaagtttttgtggatttgataatttaccttactccatcatctttgcatttagtacgtctatctttctctgaatattgtacatgctttctttcagGAGACCGCTGATCACATGCTTTATCCTAATCCTGGATCAGGAATGATACATGAACAGCATCTCCAGTTCTTTCATTTTCTCGGCAGTCTCCTCGCAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G17205.3 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G17205.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os05g06690.1 (Oryza sativa), 3'ss of exon 17
gtcatatgtctagttttgctcacccaagtttttgtggatttgataatttaccttactccatcatctttgcatttagtacgtctatctttctctgaatattgtacatgctttctttcagGAGACCGCTGATCACATGCTTTATCCTAATCCTGGATCAGGAATGATACATGAACAGCATCTCCAGTTCTTTCATTTTCTCGGCAGTCTCCTCGCAAAA
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-----aagttcaagtctgctttcctaactggtttacagtgtgatg-tctagcaatttgcatatcaattacaaa-ggctcacatgtttcgtttttaat-----------ctttttgcagGAGACAGCCGATCATCTTCTCTACCCAAATCCTGGATCTGGATTGGTCCATGAACAGCATCTGCAATACTTCCATTTTCTTGGCAGTCTCCTTGGGAAG
upper sequence: AT3G17205.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA17G04180.1 (Glycine max), 3'ss of exon 16
gtcatatgtctagttttgctcacccaagtttttgtggatt-tgataatttaccttactccatcatctttgcatttagtacgtctatctttctctgaatattgtacatgctttctttcagGAGACCGCTGATCACATGCTTTATCCTAATCCTGGATCAGGAATGATACATGAACAGCATCTCCAGTTCTTTCATTTTCTCGGCAGTCTCCTCGCAAAA
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-----------------gatcag--aagttatttcattttataatcctgctcttggtatccttatatttgttccttacgatttactgattctcggtatactgaatgttaatgtgtctagGAAACAGCGGATCACCTGCTTTATCCTAATCCTGGATCTGGAATGATACATGAACAACATTTCCAATTTTTCCACTTCCTTGGTACTCTTCTCGCAAAG
upper sequence: AT3G17205.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA09G03680.1 (Glycine max), 3'ss of exon 3
gtcatatgtctagttttgctcacccaagtttttgtggatttgataatttaccttactccatcatctttgcatttagtacgtctatctttctctgaa-tattgtacatgctttctttcagGAGACCGCTGATCACATGCTTTATCCTAATCCTGGATCAGGAATGATACATGAACAGCATCTCCAGTTCTTTCATTTTCTCGGCAGTCTCCTCGCAAAA
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----------------------------------------------------------tttttactttgtgttctattggtttatggcaatctgaaattctgaacatcattgcatccaggaaacagcagatcacctgctttatcctaatcctgga-cagGAATGATACATGAACAACATTTCCAATTTTTCCACTTTCTTGGTACTCTCCTTGCAAAG
upper sequence: AT3G17205.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA07G36390.1 (Glycine max), 3'ss of exon 16
gtcatatgtctagttttgctcacccaagtttttgtggatttgataatt-tacctt--actccatcatctttgcatttagtacgtctatctttctctgaatattgtacatgctttctttcagGAGACCGCTGATCACATGCTTTATCCTAATCCTGGATCAGGAATGATACATGAACAGCATCTCCAGTTCTTTCATTTTCTCGGCAGTCTCCTCGCAAAA
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---------------------gatcgaaagtgacttcattttataatcctgcccttggtatccttatatttgttgcttgagatttactaattctcggtatactgaatgttaatgcatttagGAAACAGCGGATCACCTGCTTTATGCTAATCCTGGATCTGGAATGATACATGAACAACATTTCCAATTTTTCCACTTCCTTGGTACTCTTCTTGCAAAG
upper sequence: AT3G17205.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv05s0077g00470.t01 (Vitis vinifera), 3'ss of exon 17
gtcatatgtctagttttgctcacccaagtttttgtggatttgataatttaccttactccatcatctttgcatttagtacgtctatctttctctgaatattgtacatgctttctttcagGAGACCGCTGATCACATGCTTTATCCTAATCCTGGATCAGGAATGATACATGAACAGCATCTCCAGTTCTTTCATTTTCTCGGCAGTCTCCTCGCAAAA
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----------aaaaacagcatgttcttgtttgagtctact---aaattggtcttgctgtattattttgccttcccgtgctttgttgatttcct---tcttg-gcttggtttaac-cagGAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgcatttagtacgtctatctttctctgaatattgtacatgctttctttcagGAGACCGCTGATCACATGCTTTATCCTAATCCTGGATCAGGAATGATACATGAACAGCATCTCCAGTTCTTTCATTTTCTCGGCAGTCTCCTCGCAAAA
tgctttctttc CT-rich tract
aatattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcatatgtctagttttgctcacccaagtttttgtggatttgataatttaccttactccatcatctttgcatttagtacgtctatctttctctgaatattgtacatgctttctttcagGAGACCGCTGATCACATGCTTTATCCTAATCCTGGATCAGGAATGATACATGAACAGCATCTCCAGTTCTTTCATTTTCTCGGCAGTCTCCTCGCAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC