Sequence
atgc intronic sequence ATGC exonic sequencegtacggtagatataatcactggttacttttatcaagttgttaggttgtttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19880.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 7
gtacggtagatataa--tcactggttacttttatcaagttgttaggttgtttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG
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---ctgttttcgtaagctagttatttagttctgtatctccctatttttatttttatttttattttttactcttttcgatt--tactaataaagaccatattgcagCCTTGTTCAATTGGATTTGCAACTGGTGGGAAGACTTTCTTTTTGTGGGGTGGCTGCATGATG
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 7
gtacggtagatataatcactggttacttttatcaagttgttaggttgtttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG
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tttgagtttttgctagaaatgtagttctttatgtgtatatcca-ttgttcatttttactattgatcatccttgcaatt--tagtgacaataaccatactgcagCCTTGTTCGATGGGATTTGCAACTGGTGGGAAGACTTTCTTCTTGTGGGGTGGCTGTATGATG
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G127754_T01 (Zea mays), 3'ss of exon 2
-gtacggtagatataatcactggttacttttatcaagttgttaggttgtttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG
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aatttttcctaggtagtgat--gtagttctttgtgtgtatgtccattgttcatttttgctattgatcatccttgcaatt--tagtgacaataaccatactgcagCCTTGCTCGATGGGATTTGCAACTGGTGGGAAGACTTTCTTCTTGTGGGG--GCTGTATGATG
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 6
----gtacggtagatataatcactggttacttttatcaagttgttaggttgtttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG----
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ttggatctgatgacttctattaatggtttttgataatatatcaatattctgatt-tgtacatactcaat--tcacttattcccatttttattttgttc----tacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G01130.1 (Glycine max), 3'ss of exon 6
gtacggtagatataatcactggttacttttatcaagt-tgttaggttgtttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttc-----cagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG----
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------tagcgatggat-ctgatgacttctattaagggtttttgataatatatcaatattctg-attgta-cttaattcacttattcctatttttattttgttctacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 7
gtacggtagatataatcactggttacttttatcaagttgttaggttg-tttataattgtagcatatcgtaatttga--gctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG
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-----gtacatattggtgatagat-ccttcaactcctgaatagattgatttgtacttattagagaaaatgtctagattgattttttttgtcttttctgatttacagCCTTGTTCGATGGGTTTCGCTACAGGTGGAAAAACATTCTTTTTGTGGGGAGGGTGTATGATG
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ38341 (Selaginella moellendorffii), 3'ss of exon 6
gtacggtagatataatcactggttacttttatcaagttgttaggttgtttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG
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--------------------------------------gtaaagactttgaaaattttgc--tctccagat----actgatatcaaga-----cgattatcagCCCTGTTCAATTGGTTTTGCGACCGGTGGAAGAACTTTCTTTTTGTGGGGCGGATGCATGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG
agctaat putative branch site (score: 3)
ttcactttcc putative PPT
taatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacggtagatataatcactggttacttttatcaagttgttaggttgtttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG