Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtctcatttctttctttgattcactaagtttagattctttctcactgcaaactttaaagacatcaccttaataaccttgagcaaatatctataccaacttttgtataaattttctgtaacttcagagctcatttgctacataaaactatattgcagGTATGTGGTGAAAACACTGGACAACGCAGAGAGTGTGAAGCTTCAGTATCGTTCATTGGCTAAAGCTCCAGAAGATCCATCAGCTAAAGCAACACCAAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G05230.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G05230.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G160304_T05 (Zea mays), 3'ss of exon 6
gtaaagtctcatttctttctttgattcactaagtttagattctttctcactgcaaactttaaagacatcaccttaataaccttgagca-aatatctataccaacttttgtataaattttctgtaacttcagagctcatttgctacataaaactatattgcagGTATGTGGTGAAAACACTGGACAACGCAGAGAGTGTGAAGCTTCAGTATCGTTCATTGGCTAAAGCTCCAGAAG---ATCCATCAGCTAAAGCAACACCAAAC
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---------------------------------------------gttagaataatctc----atcatggccttcctcgaaacaagcacaattgctatgtcactactcgtaaacctgattttttttttcatgatctatt-attactcg----cttataacagGTATGTTGTGAAGACTTCAGACAACGCAGAGAGTGTGAAGCTGCAATACCGTTCCTTGGCAAAGGTTGCTGATGGCAATGGGCCTTCTGGTCTTGTCCCA---
upper sequence: AT5G05230.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G40060.1 (Glycine max), 3'ss of exon 7
gtaaagtctcatttctttctttgattcactaagtttagattctttctcactgcaaactttaaagacatcaccttaataaccttgagcaaatatctataccaacttttgtataaattttctgtaacttcagagctcatttgctacataaaactatattgcagGTATGTGGTGAAAACACTGGACAACGCAGAGAGTGTGAAGCTTCAGTATCGTTCATTGGCTAAAGCTCCAGAAGATCCATCAGCTAAAGCAACACCAAAC
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-----------------------------------------------------------taacgctgttacaaaggaaacatggttgacattcttgttatgttactttcaaggaaatacgtaaaatttgg--ttctgttgttaacaaagacttgtgtacagGTATGTGGTGAAGACATTGGACAATGCAGAGAGTGTAAAGTTGCAGTATCGATCCCTTGCCAAGGTTATGGATGATCCTTCAAAACCTGCAGCCTCCAGC
upper sequence: AT5G05230.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv13s0067g03030.t01 (Vitis vinifera), 3'ss of exon 7
gtaaagtctcatttctttctttgattcactaagtttagattctttctcactgcaaactttaaagacatcaccttaataaccttgagcaaatatctataccaacttttgtataaattttctgtaacttcagagctcatttgctacataaaactatattgcagGTATGTGGTGAAAACACTGGACAACGCAGAGAGTGTGAAGCTTCAGTATCGTTCATTGGCTAAAGCTCCAGAAGATCCATCAGCTAAAGCAACACCAAAC
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---------------------------------------------agtattgcatgcctt---gacatgatatta----ccacaaatttctcactgtgaaaagtaccgatttaaattgccatacattta--------ttcatacaataattcat-ctacagGTATGTGGTGAAGACATTGGATAATGCAGAGAGTGTTAAACTGCAGTATCGTTCACTCGCCAAGGTTCCAGATAATCCATCCTCAAAGCCAATGTTGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtataaattttctgtaacttcagagctcatttgctacataaaactatattgcagGTATGTGGTGAAAACACTGGACAACGCAGAGAGTGTGAAGCTTCAGTATCGTTCATTGGCTAAAGCTCCAGAAGATCCATCAGCTAAAGCAACACCAAAC
ctgtaac putative branch site (score: 3)
tacataaaactatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtctcatttctttctttgattcactaagtttagattctttctcactgcaaactttaaagacatcaccttaataaccttgagcaaatatctataccaacttttgtataaattttctgtaacttcagagctcatttgctacataaaactatattgcagGTATGTGGTGAAAACACTGGACAACGCAGAGAGTGTGAAGCTTCAGTATCGTTCATTGGCTAAAGCTCCAGAAGATCCATCAGCTAAAGCAACACCAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA