Sequence
atgc intronic sequence ATGC exonic sequencegtacaatttttcctcacaactggttcataacaagtgaccattgtgtgctttatgattagaattgaattacatgccagtttaagttcatggcaaactatgatctgagttttggctttgattgttgcacttcttgaggttctggcagGTTCGACCTACAAGTGAAACCATAGTAAACCACATGTTCACTCAGTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g07060.1 (Oryza sativa), 3'ss of exon 1
-----------gtacaatttttcc-tcacaactggttcataacaa-gtgaccattgtgtgctttatgatta--gaattgaattacatgccagtttaagttcatggcaaactatgatctgagttttggctttgattgttgcacttcttgaggttctggcagGTTCGACCTACAAGTGAAACCATAGTAAACCACATGTTCACTCAGTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG
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gtaatacttccctctagtattactgttatattggatatagaaccacgattccgtgatattttccatgggcaatgattataaatacaagatgatt-gattctgtgattggattgcctctaaagctcaaccttctgcatttccattcttgagGGCTTTGTAGGTAAGACCAACTAGTGAGACCATCGTAAACCACATGTTCACCAAATGGATACAGAGCTACCGCGATCTTCCTCTCATGATTAACCAG
upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G107089_T01 (Zea mays), 3'ss of exon 3
gtacaatttttcctcacaactggt-tcataacaagtgaccattgtgtgctttatgattagaattgaattacatgccagtttaagttcatggcaaactatgatctgagttttggctttgattgttgcacttcttgaggttctggcagGTTCGACCTACAAGTGAAACCATAGTAAACCACATGTTCACTCAGTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG
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gtattactttgctctagttttatcgttaaatttggtaccagccacaaattttgttggaaaaat--gattacgt---agattgccttta-----------aacctgaacctt---ttgaacttgtg---ttcttgagggctttgtagGTAAGACCAACAAGTGAGACCATTGTAAACCACATGTTCACCAAATGGATTCAGAGCTATCGTGATCTTCCTCTCATGATAAACCAG
upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G29890.1 (Glycine max), 3'ss of exon 3
-----------gtacaatttttcctcacaactggtt-cataacaagtgaccattgt-----gtgctttatgattagaattgaa----ttacatgccagtttaagttcatggcaaactatgatctgag-ttttggctttgattgttgcacttcttgaggttctggcagGTTCGACCTACAAGTGAAACCATAGTAAACCACATGTTCACTCAGTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG
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gtatgtatgctcttcagttgtttgttacaactgctttcatgtgtgtttttcggtgtttgttgtgatatatgagatgaattgaagtgattaatcatctgtaatattgattgaaaagctgtgacctaaggttttgtctttgaattttgcacttgttgaggctgtggcagGTTCGGCCTACAAGTGAAACCATTGTGAATCATATGTTTACTCAATGGATCCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG
upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 3
----------------gtacaatttttcctcacaactgg-ttcata-acaagt-----gaccattgt-gtgctttatgattagaattga----attacatgccagtttaagttcatggcaaactatgatctgag-ttttggctttgattgttgcacttcttgaggttctggcagGTTCGACCTACAAGTGAAACCATAGTAAACCACATGTTCACTCAGTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG
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gtatgtatgctatgctctttagttgtttgttacaattgccttcatgtgcatgtattttgatatttgttgtaatatatgggatgagttgaagtgattaatcatctgtaatattgattgaaaagctgtgacctaaggttttgtctttgatttttgcacttgttgaggctgtggcagGTCCGGCCAACTAGTGAAACCATTGTGAATCATATGTTTACTCAATGGATCCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG
upper sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacaatttttcctcacaactggttcataacaagtgaccattgtgtgctttatgattagaattgaattacatgccagtttaagttcatggcaaactatgatctgag-ttttggctttgattgttgcacttcttgaggttctggcagGTTCGACCTACAAGTGAAACCATAGTAAACCACATGTTCACTCAGTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG
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---------------------------------gtaggcatttt-tctggcgttatta----tgttttac-cacaaagctagaattgtgaaaattctttgcctaaggttttgggtttgattgttgcacttgttgaggttgtggcagGTTCGGCCTACTAGTGAAACCATAGTGAATCATATGTTTACCCAGTGGATTCACAGCTATCGTGATCTTCCTCTCATGATTAATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaactatgatctgagttttggctttgattgttgcacttcttgaggttctggcagGTTCGACCTACAAGTGAAACCATAGTAAACCACATGTTCACTCAGTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG
ctttgat putative branch site (score: 5)
tttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatttttcctcacaactggttcataacaagtgaccattgtgtgctttatgattagaattgaattacatgccagtttaagttcatggcaaactatgatctgagttttggctttgattgttgcacttcttgaggttctggcagGTTCGACCTACAAGTGAAACCATAGTAAACCACATGTTCACTCAGTGGATTCATAGCTACCGTGATCTTCCTCTCATGATTAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA