Sequence
atgc intronic sequence ATGC exonic sequence...tctcctttgggaacttcaaggaggtttattttacaacattcatgtttcgtttatcagatttctttgtatcttgaaattcagtcattttgatattttccagGCAAAAGCTGATGAAATTGCAAAGCTGATGAATGAAAATGAGCAGCTAAAAATTGTAAATGAGGATTTGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g48620.1 (Oryza sativa), 3'ss of exon 2
tctcctttgggaacttcaaggaggtttattttacaacattcatg--tttcgtttatcagatttctttgtatcttgaaattcagtcattttgatattttc--cagGCAAAAGCTGATGAAATTGCAAAGCTGATGAATGAAAATGAGCAGCTAAAAATTGTAAATGAGGATTTGAAG
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----tttttacaactaagtgcatcttttacttccatattctatcatttctgcgcaacatacatacctgggcccttcacttgtctcacaacacttcttcctgcagTCCAAAGCTGATGAAATTGCAAGACTGATGAATGAGAATGAACAACTGAAATCAACAATTGATGATCTTAAG
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G168654_T01 (Zea mays), 3'ss of exon 9
------tctcctttgggaacttcaaggaggtttattttacaacattcatgtttcgtttatcagatttctttgtatcttgaaattcagtcattttgatattttccagGCAAAAGCTGATGAAATTGCAAAGCTGATGAATGAAAATGAGCAGCTAAAAATTGTAAATGAGGATTTGAAG
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taatcgtcgtttaaacgacgtttaataaccatgacttggttgcaa-cgtacccagctctttaatattcattgtgcctaacaacat-gtaattct----ctctacagTCCAAAGCTGATGAAATTGCAAGGTTGATAAATGAGAATGAGCAACTAAAATCAACAATCGATGATCTCAAG
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G01980.1 (Glycine max), 3'ss of exon 3
tctcctttgggaacttcaaggaggtttattttacaacattcatgtttcgtttatcagatttctttgtatcttgaaat---tcagtcattttgatat--tttccagGCAAAAGCTGATGAAATTGCAAAGCTGATGAATGAAAATGAGCAGCTAAAAATTGTAAATGAGGATTTGAAG
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--tttttttgtaatt--atgctcctcttctatatg-ctttttttctttggccattatattgttgcatatcttattatgtttttgtaatcttgcttctctttgcagGCTAAAGCTGATGAGATTGCAAAATTGATGAATGAAAATGAACAATTGAAAGCCGTGATTGAGGATTTCAAG
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G43330.1 (Glycine max), 3'ss of exon 5
tctcctttgggaacttcaaggaggtttattttacaacattcatgtttcgtttatcagatttctttgtatcttga---aattcagtcattttgatat--tttccagGCAAAAGCTGATGAAATTGCAAAGCTGATGAATGAAAATGAGCAGCTAAAAATTGTAAATGAGGATTTGAAG
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-----ttttctaattatgctactcttctatatgctgttttttttttgtggccattatattgttgcatatattattacattttcttaatattggttctctttgcagGCTAAAGCTGATGAGATTGCAAAATTGATGAATGAAAATGAACAATTGAAAGCTGTGATTGAGGATTTCAAG
upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 3
-tctcctttgggaacttcaaggaggtttattttacaacattcatgtttcgtttatcagatttctttgtatcttgaaattcagtcattttgatattttccagGCAAAAGCTGATGAAATTGCAAAGCTGATGAATGAAAATGAGCAGCTAAAAATTGTAAATGAGGATTTGAAG
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gtacatctttagatcctcatgaaaggttttgctacggatatggtgcttc-tataccaattttctggggatttg---------------------tttacagGCAAAGGCTGATGAGATTGCGAAGTTGATGCATGAAAATGAGCAGCTAAAATCTGTCACTGAGGATTTGAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|34544079|gb|CF512311.1|CF512311EST: AGATGAAGATGCTGGAAACTGCACTCCAGGGGGCTGCAAGACAAGCTCAG GCAAAAGCTGATGAAATTGCAAAGCTGATGAATGAAAATGAGCAGCTAAAA
genomic: AGATGAAGATGCTGGAAACTGCACTCCAGGGGGCTGCAAGACAAGCTCAGgtacattatt ... tattttccagGCAAAAGCTGATGAAATTGCAAAGCTGATGAATGAAAATGAGCAGCTAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgtttatcagatttctttgtatcttgaaattcagtcattttgatattttccagGCAAAAGCTGATGAAATTGCAAAGCTGATGAATGAAAATGAGCAGCTAAAAATTGTAAATGAGGATTTGAAG
ttttgat putative branch site (score: 4)
tattttcc CT-rich tract
tcattttgatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctcctttgggaacttcaaggaggtttattttacaacattcatgtttcgtttatcagatttctttgtatcttgaaattcagtcattttgatattttccagGCAAAAGCTGATGAAATTGCAAAGCTGATGAATGAAAATGAGCAGCTAAAAATTGTAAATGAGGATTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - cattcat