Sequence
atgc intronic sequence ATGC exonic sequence...ggttgactggcctttccctttctgcactgttgcagatattgaatagtttgtgctcttttgcattgttgatgaattggttttgttgctatgctttttgcagGGATCCAGATCATGACAAGGGCTCAAACCTGCCATCCGTTGGACCCATTATCTGCAACTGAAATCTCAGTGGCTGTGGCAACTGTCAGAGCTGCTGGAGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 1
----ggttgactggcctttccctttctgcactgttgcagatattgaatagtttgtgctcttttgcattgttgatgaattggttttgt-tgctatgctttttgcagGGATCCAGATCATGACAAGGGCTCAAACCTGCCATCCGTTGGACCCATTATCTGCAACTGAAATCTCAGTGGCTGTGGCAACTGTCAGAGCTGCTGGAGC
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gtgtatttggatagtttaatattttctgttcaatt-taagcatc-agtacatag--ctatgctatatcac-aatgacttgacgttatgcgggagaaacatttcagGAATCCGGATCATGACGAGGACACAGAAAAGCCACCCCTTAGACCCACTATCTGCTGCTGAAATTTCTGTGGCTGTAGCAACTGTCAGAGCTTCTGGAAG
upper sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 2
-ggttgactggcctttccctttctgcactgttgcagatattgaatagtttgtgctcttttgcattgttgatgaattggttttgttgctatgctttttgcagGGATCCAGATCATGACAAGGGCTCAAACCTGCCATCCGTTGGACCCATTATCTGCAACTGAAATCTCAGTGGCTGTGGCAACTGTCAGAGCTGCTGGAGC
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aagttgtttgag-tgacctgttcagcatacatgtcttaattgaattatattcattattattacccgtttctaatgttctgctggatggaacaaaatggcagGGATACCTATAATGACCAGAGCCCAGAGAAGCCACCCTTTAGATCCATTATCTGCTGCTGAAATTGCAGTGGCTATAGCAACTGTAAGAGCTGCTGGAAA
upper sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 1
ggttgactggcctttccctttctgcactgttgcagatattgaatagtttgtgctcttttgcat-tgttga-tgaattggttttgttgctatgctttt--tgcagGGATCCAGATCATGACAAGGGCTCAAACCTGCCATCCGTTGGACCCATTATCTGCAACTGAAATCTCAGTGGCTGTGGCAACTGTCAGAGCTGCTGGAGC
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---ttaccattttcaacagcctataacctagatagacacatacta-tttgaaatgtgtaccatgtgttaactgaactactgtttatcttgagaaaaaaatgcagGGATACCAATAATGACAAGAGCCCAGAGGTGTCACCCTTTGGACCCATTATCTGCTGCTGAAATTGCAGTTGCTGTAGCAACTGTAAGAGTTGCTGGAAG
upper sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 1
ggttgactggcctttccctttc---tgcactgttgcagatattgaatagttt-gtgctcttttgcatt-gttga-tgaattggttttgttgctatgct-ttttgcagGGATCCAGATC---ATGACAAGGGCTCAAACCTGCCATCCGTTGGACCCATTATCTGCAACTGAAATCTCAGTGGCTGTGGCAACTGTCAGAGCTGCTGGAGC
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-------caattttttatttgcaagttcttgaatgcaggctttgcttgttttcatgttttttaatattagctaactgtgtttctatttttgttgtaatgttgcatagGAGTCGTTGCTGCAATGCCAAGGGCACAGTCAAGCCACCCTTTGGATCCTTTATCTGCTGCTGAAATCTCTGTGGCTGTGGCAACTGTGCGGGCTGCTGG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgtgctcttttgcattgttgatgaattggttttgttgctatgctttttgcagGGATCCAGATCATGACAAGGGCTCAAACCTGCCATCCGTTGGACCCATTATCTGCAACTGAAATCTCAGTGGCTGTGGCAACTGTCAGAGCTGCTGGAGC
tgttgat putative branch site (score: 4)
tgcttttt putative PPT
atgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggttgactggcctttccctttctgcactgttgcagatattgaatagtttgtgctcttttgcattgttgatgaattggttttgttgctatgctttttgcagGGATCCAGATCATGACAAGGGCTCAAACCTGCCATCCGTTGGACCCATTATCTGCAACTGAAATCTCAGTGGCTGTGGCAACTGTCAGAGCTGCTGGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- -tgactgg
- - - - - - - -ccctttc
- - - - - - - - - - - - - - - tgcagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct