Sequence
atgc intronic sequence ATGC exonic sequencegtaaagctctattcatcgctgagatcttacaccagccactgtgagtagagtattagcttatgacacatgatatgtttactcttgcagGCGGCTGTGGCTCAAGCTGCATTAGCATACAAGCTATACCAGCAGAAATTCTCTGGCCCAAGATGGGAAGCTCTGGTAAAGAAAGGTGCCAAGAAACAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13420.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g70170.1 (Oryza sativa), 3'ss of exon 4
----------gtaaagctctattcatcgctgagatcttacaccagccactgtgagtagagtattagcttatgacacatgatatgtttactcttgcagGCGGCTGTGGCTCAAGCTGCATTAGCATACAAGCTATACCAGCAGAAATTCTCTGGCCCAAGATGGGAAGCTCTGGTAAAGAAAGGTGCCAAGAAACAGA
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gtacgcacaatcaaaattacatgcctc-ctaagtcctagcattaggaatttccaaactagcagttctaatctgcattttggtcactctgtattacagGCTGCTGTAGCACAGGCAAAGCTAGCCAACCAGCTTTACCAGAAGAAATTCTCTGGCCCGAGGTGGGAGGCTTTGGTCAAGAAAGGTGCCAAGAAGCAGA
upper sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G134256_T02 (Zea mays), 3'ss of exon 3
gtaaagctctattcatcgctgagatcttacaccagccactgt-gagtagagtattagcttatgacacatgat-atgtttactcttg-cagGCGGCTGTGGCTCAAGCTGCATTAGCATACAAGCTATACCAGCAGAAATTCTCTGGCCCAAGATGGGAAGCTCTGGTAAAGAAAGGTGCCAAGAAACAGA-------------------------
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---------------taactgcctcttgatgttagaaacttttaaactgtccacaaagttatgcaatatgaccatactctatcatgtcaggctgcagtagcacaggccaaactagCAAATCGGCTCTACCAGAAGAAATTCTCTGGCCCAAGGTGGGAGGCGTTGGCCAAGAAAGGTGCCAAGAAACAAAGGTTGTTGTGGGCATCCACCGGTGT
upper sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G134256_T01 (Zea mays), 3'ss of exon 4
----gtaaagctctattcatcgctgagatcttacaccagccactgt-gagtagagtattagcttatgacacatgat-atgtttactcttg-cagGCGGCTGTGGCTCAAGCTGCATTAGCATACAAGCTATACCAGCAGAAATTCTCTGGCCCAAGATGGGAAGCTCTGGTAAAGAAAGGTGCCAAGAAACAGA
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gtaaacaaaactataatta--actgcctcttgatgttagaaacttttaaactgtccacaaagttatgcaatatgaccatactctatcatgtcagGCTGCAGTAGCACAGGCCAAACTAGCAAATCGGCTCTACCAGAAGAAATTCTCTGGCCCAAGGTGGGAGGCGTTGGCCAAGAAAGGTGCCAAGAAACAAA
upper sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G828312_T02 (Zea mays), 3'ss of exon 1
gtaaagctctattcatcgctgagatcttacaccagccactgtgagtagagtattagcttatgacacatgatatgtttactcttgcagGCGGCTGT-GGCTCAAGCTGCATTAGCATACAAGCTATACCAGCAGAAATTCTCTGGCCCAAGATGGGAAGCTCTGGTAAAGAAAGGTGCCAAGAAACAGA--------------------------------------------------------------
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--------------------------------------------------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaggctgccgttggcacaggcccaactagcaaatcgggtctaccagaagaaattctctggcccgagGTGGGAGGCGTTGGCCAAGAAAGGTGCCAAGAAACAGAGGTTGTTGTGGGCATCCACCCGGTGTCAAGAACCCAGCTTATCCCGACACTCTTTACATCGA
upper sequence: AT5G13420.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0150g00190.t01 (Vitis vinifera), 3'ss of exon 5
gtaa-agctctattcatcgctgagatcttacaccagccactgtgagtagagtattagcttatgacacatgatatgtttactcttgcagGCGGCTGTGGCTCAAGCTGCATTAGCATACAAGCTATACCAGCAGAAATTCTCTGGCCCAAGATGGGAAGCTCTGGTAAAGAAAGGTGCCAAGAAACAGA
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gtaataaattaatttacaatcaaattgtcatccttttgagggtttaaaactcaggacctaatatcatgggacttttata-tgttctagGCTGCAGTAGCTCAAGCAGCACTGGCATACCAGCTCTACCAGAAGAAATTCTCTGGGCCTAGATGGGAAGCTCTGGTGAAGAAAGGTGCCAAGAAACAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagccactgtgagtagagtattagcttatgacacatgatatgtttactcttgcagGCGGCTGTGGCTCAAGCTGCATTAGCATACAAGCTATACCAGCAGAAATTCTCTGGCCCAAGATGGGAAGCTCTGGTAAAGAAAGGTGCCAAGAAACAGA
tttactctt CT-rich tract
atatgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagctctattcatcgctgagatcttacaccagccactgtgagtagagtattagcttatgacacatgatatgtttactcttgcagGCGGCTGTGGCTCAAGCTGCATTAGCATACAAGCTATACCAGCAGAAATTCTCTGGCCCAAGATGGGAAGCTCTGGTAAAGAAAGGTGCCAAGAAACAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA