Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaagtgtactagattatctgttttatacggtagacatggaaccaacaatctccttttcaatattctgtttttccttcctatgagctgtctgattgctgcatttgtagtgttgaatgtctgaactgatggtcttactcttaatggcctcagGGCAGTCCCAGCCACCATGCCATCTTTCAGTATTTCTTGAAGTGACAGATTCACGAAGCTCAAGTGATTGGAGCTGTTTTGTTAGCCACCGACTATCAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G25320.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G25320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G07050.1 (Glycine max), 3'ss of exon 1
gtatgtaagtgtactagattatctgttttatacggtagacatggaaccaacaatctccttttcaatattctgtttttccttcctatgagctgtctgattgctgcatttgtagtgttgaatgtctgaa-ctgatgg-tcttac----tcttaatggcctcagGGCAGTCCCAGCCACCATGCCATCTTTCAGTATTTCTTGAAGTGACAGATTCACGAAGC---TCAAGTGATTGGAGCTGTTTTGTTAGCCACCGACTATCAGT
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----------------------------------------------------------tgtgccttacactcagattatttttaatacactgagagtatgtt---tttgttgtgataaaagatggagtctgatgaattttatatgattttggtgctatcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTGTTTCTTGAAGTTACAGATTCAAGAAATACTTCCAGTGATTGGAGTTGTTTTGTAAGTCATCGTTTGTC---
upper sequence: AT2G25320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G06960.1 (Glycine max), 3'ss of exon 1
gtatgtaagtgtactagattatctgttttatacggtagacatggaaccaacaatctccttttcaatattctgtttttccttcctatgagctgtctgattgctgcatttgtagtgttgaatg---tctgaactgatggtcttac--tcttaatggcctcagGGCAGTCCCAGCCACCATGCCATCTTTCAGTATTTCTTGAAGTGACAGATTCACGAAGC---TCAAGTGATTGGAGCTGTTTTGTTAGCCACCGACTATCAGT
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--------------------------------------------------------tgtgtcttacactcagattattttg---atacacctagaatttgtttagtttgtgataaaaaatggagtctga-tgaatttttatacgattttggtgctatcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTGTTTCTTGAAGTTACTGATTCAAGAAATACTTCCAGTGATTGGAGTTGTTTTGTAAGTCATCGTTTGTC---
upper sequence: AT2G25320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0008g05690.t01 (Vitis vinifera), 3'ss of exon 1
gtatgtaagtgtactagattatctgttttatacggtagacatggaaccaacaatctccttttcaatattctgtttttccttcctatgagctgtctgattgctgcatttgtagtg--ttgaatgtctgaactgatgg-tcttactcttaatggcctcagGGCAGTCCCAGCCACCATGCCATCTTTCAGTATTTCTTGAAGTGACAGATTCACGAAGC---TCAAGTGATTGGAGCTGTTTTGTTAGCCACCGACTATCAGT
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---------------------------------------------------------cttctcattttaccctgaggatttccattgagtctttttgt-gctagactaccagttgcttaggaaagtgacctgatgaaccctatgcttgatggtttcagGGCAGTCTCAGCCACCATGCCACCTTTCAGTCTTTCTCGAGGTTACAGATTCACGAAATACTTCCAGTGATTGGAGTTGTTTTGTGAGCCACCGATTGTC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcatttgtagtgttgaatgtctgaactgatggtcttactcttaatggcctcagGGCAGTCCCAGCCACCATGCCATCTTTCAGTATTTCTTGAAGTGACAGATTCACGAAGCTCAAGTGATTGGAGCTGTTTTGTTAGCCACCGACTATCAGT
tcttaat putative branch site (score: 3)
tcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaagtgtactagattatctgttttatacggtagacatggaaccaacaatctccttttcaatattctgtttttccttcctatgagctgtctgattgctgcatttgtagtgttgaatgtctgaactgatggtcttactcttaatggcctcagGGCAGTCCCAGCCACCATGCCATCTTTCAGTATTTCTTGAAGTGACAGATTCACGAAGCTCAAGTGATTGGAGCTGTTTTGTTAGCCACCGACTATCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT