Sequence
atgc intronic sequence ATGC exonic sequencegtacgtgaactcagtgtctctcttttatttttcttgtctatatcttctgcaactatttatagtttgtgtctttagttaaagatgtattctgttttcatctttgactctcttttttttttttttttttttaattctgctatggtttagGTACACTTCGAAGATGCTTCTATCTGCTATTGACGAGCATTGTAAAGGAACTTATGATTTCCTTTATTTGCCAATTGACTTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G61960.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
gtacgtgaactcagtgtctctcttttatttttcttgtctatatcttctgcaactatttatagtttgtgtctttagttaaagatgtattctgttttcatctttgactctcttttttttttttttttttttaattctgctatggttt-agGTACACTTCGAAGATGCTTCTATCTGCTATTGACGAGCATTGTAAAGGAACTTATGATTTCCTTTATTTGCCAATTGACTTCAAG
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------------------------------------------gtatgtgtaacaactgttaatttaggttcatttttt------tttcttgcctttgccttc--ttttctgtcattttcatgtatttctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 11
gtacgtgaactcagtgtctctcttttatttttcttgtctatatcttctgcaactatttatagtttgtgtctttagttaaagatgtattctgttttcatctttgactctcttttttttttttttttttttaattctgctatggtttagGTACACTTCGAAGATGCTTCTATCTGCTATTGACGAGCATTGTAAAGGAACTTATGATTTCCTTTATTTGCCAATTGACTTCAAG
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----------------------------------------aaattttagaggcagtaaagaattcatactctc--ttgcattagtctcccgatttgacttgtttctgtttttttatttatttatttgcta--tttgtt-tggt--agGTATACTTCAAAGATGCTTCTTGCTGCAATAGACGAGCAATGTAAAGGAACTTATGATTTTCTGTATTTACCGATTGATTTCAAG
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 7
gtacgtgaactcagtgtctctcttttatttttcttgtctatatcttctgcaactatttatagtttgtgtctttagttaaagatgtattctgtt---ttcatctttga--ctctcttttttttttttttttttttaattctgctatggtttagGTACACTTCGAAGATGCTTCTATCTGCTATTGACGAGCATTGTAAAGGAACTTATGATTTCCTTTATTTGCCAATTGACTTCAAG
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-----------------------------------------------tacaa--aatttgaataacaatttttaaaaacaagcaaattcttttgcactggtctttcagtttgtctctttcatttatatttgtttaaatatttt-tggc--agGTATACTTCAAAGATGCTTCTTGTTGCCATAGATGAGCAATGTCGAGGAACTTATGATTTTCTGTATTTGCCAATTGATTTCAAG
upper sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 11
gtacgtgaactcagtgtctctcttttatttttcttgtctatatcttctgcaactatttatagtttgtgtctttagttaaagatgtattctgttttcatctttgactctcttttttttttttttttt--tttaattctgctatggtt-tagGTACACTTCGAAGATGCTTCTATCTGCTATTGACGAGCATTGTAAAGGAACTTATGATTTCCTTTATTTGCCAATTGACTTCAAG
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-------------------------------------------------cattcatttcta-tttgtggttttacacaccataattgctcagattcctgttgcatcctctgttatttctgccttttgatttgatataatggtaattgtagGTATACTTCAAAAATGCTTCTTGCTGCAATTGATGAACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcatctttgactctcttttttttttttttttttttaattctgctatggtttagGTACACTTCGAAGATGCTTCTATCTGCTATTGACGAGCATTGTAAAGGAACTTATGATTTCCTTTATTTGCCAATTGACTTCAAG
ttttaat putative branch site (score: 3)
tttgactctctttttt CT-rich tract
tttttttttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtgaactcagtgtctctcttttatttttcttgtctatatcttctgcaactatttatagtttgtgtctttagttaaagatgtattctgttttcatctttgactctcttttttttttttttttttttaattctgctatggtttagGTACACTTCGAAGATGCTTCTATCTGCTATTGACGAGCATTGTAAAGGAACTTATGATTTCCTTTATTTGCCAATTGACTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA