Sequence
atgc intronic sequence ATGC exonic sequencegtaccctgaaacaaagaaaacccttttcaagttcttattcattaagtctcatactgtttaaatctgtactgatgattttgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06370.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 4
--------gtaccctgaaacaaagaaaacccttttcaagttcttattcattaagtctcatactgtttaaatctgtac-tgatgattttgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA-----------------------------------------------------
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gtcagttcttatatgaacctaatgcgtaagcatttcgattgcatgcctgtggttctgtgttttgacttgttccgcatgtgaacttttttcagCACTTGGGGCAATATTCTCGGCAACAGACTCTGTATGCACCTTGCAGGTTTTGAACCAAGATGAAACACCCTTCTTGTACAGCCTGGTTTTCGGGGAAGG
upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G070594_T01 (Zea mays), 3'ss of exon 2
---gtaccctgaaacaaagaaaacccttttcaagttcttattcattaagtctcatactgtttaaatctgtactgatgattttgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA-----------------------------------------------------
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gtaagttcatcacccaaagcataaacacttatgttgcccatatac--agttctttctttctgactcttgtacatcttaaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAATATGAGACACCATTCTTGTACAACCTCGTGTTTGGTGAAGG
upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G037342_T02 (Zea mays), 3'ss of exon 4
---gtaccctgaaacaaagaaaacccttttcaagttcttattcattaagtctcatactgtttaaatctgtactgatgattttgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA-----------------------------------------------------
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gtaagttcatcacccaaagcataaacacttctgttgcccatatac--agttctttctttctgactcttgtacatcttaaatttcagCACTTGGGGCAATATTCTCGGCCACAGACTCGGTTTGCACCTTGCAGGTGTTAAGCCAAGATGAGACACCATTCTTGTACAGCCTCGTGTTTGGTGAAGG
upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G38160.1 (Glycine max), 3'ss of exon 4
-----------gtaccctgaaacaaagaaaaccctt---ttcaagttcttattcattaagtc----tcatactgtttaaatctgtactgatgattt-------tgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA
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gtgtgcttaaattaccttcttttacagtaatttgttggacttaactccaaacttggaacattcccttcttccctcctatatctacttacctgagtcaactgaatgcagCAATTGGAGCAATATTTTCAGCAACAGATTCTGTTTGCACGTTGCAG
upper sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------gtaccctgaaacaaagaaaacccttttcaagt-tcttattc--attaagtctcatactgtttaaatctgtactgatgattttgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA
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gtactcttcatttcacactttgctccccaaaagttctttgtgtcccaaaagttctttgtgttttctcttattacaatttcatttcttgttctctca-tctcactcaatgattt-gcagCACTTGGAGCAATATTTTCTGCAACAGATTCCGTTTGCACATTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttcttattcattaagtctcatactgtttaaatctgtactgatgattttgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA
tactgat putative branch site (score: 2)
ttattcattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccctgaaacaaagaaaacccttttcaagttcttattcattaagtctcatactgtttaaatctgtactgatgattttgcagCCATTGGAGCAATATTCTCTGCTACAGACTCTGTTTGCACCTTGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA