Sequence
atgc intronic sequence ATGC exonic sequence...ttcaccatatatatatatatatatgtttctttcttcctgtgtagaactgtttcacgagctccgggtattgatatgaacaataggaatttcaattgtatagGGTTTTAGAAAGGTTGATCCAGACAGATGGGAGTTTGCAAATGAAGAGTTTCTCAGAGGACAAAAGCCTCTGTTGAAGAAAATCAAGAGGAAGAAGGCAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g04090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G010871_T05 (Zea mays), 3'ss of exon 2
------------------------ttcaccat-atatatatatatatatgtttctttcttcctgtgtagaactgtttc---acgagctccgggtattgatatgaac-----aataggaatttcaattgtat----------agGGTTTTAGAAAGGTTGATCCAGACAGATGGGAGTTTGCAAATGAAGAGTTTCTCAGAGGACAAAAGCCTCTGTTGAAGAAAATCAAGAGGAAGAAGGCAC
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gtatattgctggcctatcattatccctgttattgcagatataaatatacaaaagctgaaatttacagagaacctcatccaagcgaacataatgccttatgactgacctgctgatgaccatttctggtctattgcaacctgcagGGCTTCAGAAAGGTTGATCCTGACAGGTGGGAGTTTGCAAATGAAGGTTTCCTCAGAGGTCAAAGGCACCTGCTGAAGATGATAAAGAGAAGGAAGCCAC
upper sequence: Vv05s0020g04090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G010871_T03 (Zea mays), 3'ss of exon 1
-ttcaccatatatatatatatatatgtttctttcttcctgtgtaga-actgtttcacgagctccgggtattgatatgaacaatagga--atttcaattgtatagGGTTTTAGAAAGGTTGATCCAGACAGATGGGAGTTTGCAAATGAAGAGTTTCTCAGAGGACAAAAGCCTCTGTTGAAGAAAATCAAGAGGAAGAAGGCAC
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atatacaaaagctgaa-atttacagagaacctcatccaagcgaacataatgccttatgactgacc--tgctgatgaccatttctggtctattgcaacc-tgcagGGCTTCAGAAAGGTTGATCCTGACAGGTGGGAGTTTGCAAATGAAGGTTTCCTCAGAGGTCAAAGGCACCTGCTGAAGATGATAAAGAGAAGGAAGCCAC
upper sequence: Vv05s0020g04090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G132971_T01 (Zea mays), 3'ss of exon 1
-ttcaccatatatatatatatatatgtttctttcttcct--gtgtagaactgtttcacgagctccgggtattgatatgaacaataggaatttcaattgtatagGGTTTTAGAAAGGTTGATCCAGACAGATGGGAGTTTGCAAATGAAGAGTTTCTCAGAGGACAAAAGCCTCTGTTGAAGAAAATCAAGAGGAAGAAGGCAC
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ttatccaatctgaaatgatttcagcagttaattcttcctcaatgaaaaatggcgattgatatttctggt---gactggattagcggattatttggtttggcagGGCTTCAGAAAGGTGGATCCTGACAGATGGGAATTTGCTAATGAGGAGTTTCTGAGAGGTCAGAGGCACCTCCTCAAAAACATTAGGCGTCGGAAACCTC
upper sequence: Vv05s0020g04090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G00560.1 (Glycine max), 3'ss of exon 1
----ttcaccatatatatatatatatatgtttctttcttcctgtg-tagaactgtttcacgagctccgggtattgatatgaacaataggaatttcaattgtatagGGTTTTAGAAAGGTTGATCCAGACAGATGGGAGTTTGCAAATGAAGAGTTTCTCAGAGGACAAAAGCCTCTGTTGAAGAAAATCAAGAGGAAGAAGGCAC
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ggggttcttaagatatgcctctctcaattcttttttgccatagtgatgataagatgttatggatttgaaaagaaggaataac---ttggtgttgtacttgta--gGGGTTTAGAAAGGTAGATCCGGATAAGTGGGAGTTTGCTAATGAAGGGTTTCTTAGAGGACAGAAGCATCTATTGAAGAACATAAGGAGAAAGAAGACAT
upper sequence: Vv05s0020g04090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G28870.1 (Glycine max), 3'ss of exon 1
ttcaccatatatatatatatatatgtttctttcttcctgtgtagaactgtttcacgagctccgggtattgatatgaacaataggaatttca------attgtatagGGTTTTAGAAAGGTTGATCCAGACAGATGGGAGTTTGCAAATGAAGAGTTTCTCAGAGGACAAAAGCCTCTGTTGAAGAAAATCAAGAGGAAGAAGGCAC
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--tataagagttttat-cacatgcatttgtcaaaccattattacagcgatatt-tgatatatagatttgaaaatgaagaa--ggaatttgatgacatgatctgtagGGGTTTAGAAAGGTTGATCCAGATAAGTGGGAGTTTGCTAATGAGTTGTTTCTTAGAGGGCAAAAGATTCTTCTGAAGAACATTAGAAGGAGGAAAGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtttcacgagctccgggtattgatatgaacaataggaatttcaattgtatagGGTTTTAGAAAGGTTGATCCAGACAGATGGGAGTTTGCAAATGAAGAGTTTCTCAGAGGACAAAAGCCTCTGTTGAAGAAAATCAAGAGGAAGAAGGCAC
tattgat putative branch site (score: 3)
aatttcaattgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaccatatatatatatatatatgtttctttcttcctgtgtagaactgtttcacgagctccgggtattgatatgaacaataggaatttcaattgtatagGGTTTTAGAAAGGTTGATCCAGACAGATGGGAGTTTGCAAATGAAGAGTTTCTCAGAGGACAAAAGCCTCTGTTGAAGAAAATCAAGAGGAAGAAGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
ttcacca
- - - - - - - - - - - - - - - - -ttcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaata