Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttcttttatttcttatgtaaatgaaaagccctgatacctcaataatcttccgtttctctgccagttgttttgtatttacatgttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G25780.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os10g41960.1 (Oryza sativa), 3'ss of exon 8
gtatgtttcttttatttcttatgtaaatgaaaagccctgatacctcaataatcttccgttt-ctctgccagttgtt--ttgtatttacatgttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
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----------------------gtaagtgcaattttctg-tgcttcatcccttttgaggaagttccgtcaactaatggtgaagactaaaatctataatttttattgaaagGTGAGCCTTGTGCAAATTCCTGGCAAAGAGGAGCTGCGGCAGAAAAACCTTTTCAGTGTCAGTGATTGCAAGATGTACTGGCAGAACAGTGGAGAATATC
upper sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA04G06080.1 (Glycine max), 3'ss of exon 11
----gtatgtttcttttatttcttat--gtaaatgaaaa---------gccctgatacctcaataatcttccgt---ttctctgccagttgttttgtatttacatgttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
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gtaagtatgtattttttctttcatgtaggtctattgaagttttattttacttggttattgtaatgaatggtcatatattatttattaattattttatatttatgttctt-tgacatatttat-agGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCGGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
upper sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G00470.1 (Glycine max), 3'ss of exon 8
----gtatgtttcttttatttct-tatgtaaatgaaaa---------gccctgatacctcaataatcttccgt---ttctctgccagttgttttgtatttacatgttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
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gtaagtgtgtttttttctttcatgtatgtggtttaaagttttgttttacttgggtatcataatgaatggtcttatattatttatcaattattatatatatgttctttgacata----tttatagGTTAGTCTGATTCAAATCCCCAGCAAAGTGGAACTCAGGCAGAAAAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAATGGAGACTACC
upper sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G14870.1 (Glycine max), 3'ss of exon 8
gtatgttt-cttttatttcttatgtaaatga---aaagccctg----------atacctcaataatcttccgt---ttctctgccagttgttttgtatttacatg--ttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
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gtaagtttgtctttttctttcatgtacatggattaaagttttgttttacttgggtatcataatgaatggtcatatattatttatcaattattttatatctatgttctttgatata----tttatagGTTAGTCTGATTCAAATCCCCAGCAAAGAGGAACTCAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATTTACTGGCAAAGCAATGGAGACTACC
upper sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 8
-------------------gtatgtttcttttatttcttatgtaaatgaaaagccctgatacctcaataatcttccgtttctctgcca-------gttgttttgtatttacatgttgatatcccat----tcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
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gtgagtgcagctgttccatgcaaaaccagttt-tctcttctttttatattttgcttctcttcctt--taatattttgcttctcttccatagacaagttaaaatttgattaatggtctttacttcataaaatatgcagGTGAGTCTGGTTCAAATCCCCAGTAAAGAGGAGTTGAGGCAGAAGAATCTCTTTAGTGTTAGTGACTGCAAAATGTACTGGCAAAGCAATGGGGACTACC
upper sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ13839 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtttcttttatttcttatgtaaatgaaaagccctgatacctcaataatcttccgtttctctgccagttgttttgtatttacatgttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
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---------------------------------------gtatgt-atttgtgtttgatttctctacatgtgacctgg--tttgc-tcttgac------ttcaacagGTTAGCCTGGTTCAAATTCCTGGCAGGGAAGAACTGAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAACGGAGACTATC
upper sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ12681 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtttcttttatttcttatgtaaatgaaaagccctgatacctcaataatcttccgtttctctgccagttgttttgtatttacatgttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
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---------------------------------------gtatgt-atttgtgtttgatttctctacatgtgacctggt---------ttgctctcaacttcaacagGTCAGCCTGGTTCAAATTCCTGGCAGGGAAGAACTGAGGCAGAAGAACCTTTTCAGTGTCAGTGACTGCAAGATGTACTGGCAAAGCAACGGAGACTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttccgtttctctgccagttgttttgtatttacatgttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
tgttgat putative branch site (score: 4)
tcccattcttc CT-rich tract
ttgttttgtattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttcttttatttcttatgtaaatgaaaagccctgatacctcaataatcttccgtttctctgccagttgttttgtatttacatgttgatatcccattcttcagGTTGCTCTAGTCCAAATCCCGAGTAAGGTAGAGCTGAGGCAGAAGAATCTCTTCAGTGTGAGCGACTGCAAGATGTACTGGCAGAGTAGTGGAGAGTATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA