Sequence
atgc intronic sequence ATGC exonic sequence...gttacaagttattgcaatgcctattactgttaattctgatagtgactaaactttccacttctttttttttctctccctatcgtttttgcgattctttcagAGACAGCATTAAAACTTGACAGTTTGGTTGGTGACATCGAAGATGCTGTATCTTCTACTATGAACAGAAATCTAAAGAAGCATGCTTCCACACACAGTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g05940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G036418_T01 (Zea mays), 3'ss of exon 2
--gttacaagttattgcaatgcctattactgttaattctgatagtgactaaactttccacttctttttttttctctccctatcgtttttgcgattctttcagAGACAGCATTAAAACTTGACAGTTTGGTTGGTGACATCGAAGATGCTGTATCTTCTACTATGAACAGAAATCTAAAGAAGCATGCTT-CCACACACAGTTC
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acatcccattctcttggcttgtttttgagtgaagtttctg-cagt-actttatttttaactttgcaattggtgtgttcttaccggtaggttgtcctatacagAAATGGCTCTCAAACTTGACAGTTTGGTGGGTGATATAGAAGATGCAGTTTCTTCTTCTGTTACTGGAAAACTTAAATCTCGTGTAGACAATTCGGAG---
upper sequence: Vv17s0000g05940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G036418_T02 (Zea mays), 3'ss of exon 2
----------------gttacaagttattgcaatgcctattactgttaattctgatagtgactaaactttccacttctttttttttctctccctatcgtttttgcgattctttcagAGACAGCATTAAAACTTGACAGTTTGGTTGGTGACATCGAAGATGCTGTATCTTCTACTATGAACAGAAATCTAAAGAAGCATGCTTCCACACACAGTTC
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cattatttacatttacatcccattctcttggcttgtttttgagtgaagtttctg-cagt-actttatttttaactttgcaattggtgtgttcttaccggtagGTTGTCCTATACAGAAATGGCTCTCAAACTTGACAGTTTGGTGGGTGATATAGAAGATGCAGTTTCTTCTTCTGTTACTGGAAAACTTAAATCTCGTGTA--------------
upper sequence: Vv17s0000g05940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G47180.1 (Glycine max), 3'ss of exon 2
-gttacaagttattgcaatgcctattactgttaattctgatagtgactaaactttccacttctttttttttctctccctatcgtttttgcgattctttcagAGACAGCATTAAAACTTGACAGTTTGGTTGGTGACATCGAAGATGCTGTATCTTCTACTATGAACAGAAATCTAAAGAAGCATGCTTCCACACACAGTTC---
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tttcagtgatggttatcatactgtgtttggtttgatttcttaggtgttac-cttttggttaatgttgtttgattcttgaaactcctttgtttgtctttcagAGACAGCACTGAAACTTGATACTTTGGTTGGTGATATTGAGGATGCTGTATCATTTACCATGAGCAAGAACATAAGGAAACAT---TCTAGTCAAAATTCACA
upper sequence: Vv17s0000g05940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G25590.1 (Glycine max), 3'ss of exon 2
-gttacaagttattgcaatgcctattactgttaattctgatagtgactaaactttccacttctttttttttctctccctatcgtttttgcgattctttcagAGACAGCATTAAAACTTGACAGTTTGGTTGGTGACATCGAAGATGCTGTATCTTCTACTATGAACAGAAATCTAAAGAAGCATGCTTCCACACACAGTTC---
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tttcagtgatgattatcatactgtgtttggtttaatttcttaggtgttac-ctttttgtgaatgttgtttgattcttgaaactcctttgtttgtctttcagAGAAAGCACTGAAACTTGATACTTTGGTTGGTGATATTGAGGATGCTGTATCATTTACCATGAGCAAGAACATAAGGAAACAT---TCTAGTCAAAATTCACA
upper sequence: Vv17s0000g05940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G47700.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------gttacaagttattg----caatgcctattactgttaattctgatagtgactaaactttcca--cttcttttttt-ttctctccctatcgt--------ttttgcgat---------tctttcagAGACAGCATTAAAACTTGACAGTTTGGTTGGTGACATCGAAGATGCTGTATCTTCTACTATGAACAGAAATCTAAAGAAGCATGCTTCCACACACAGTTC---
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gtatgtttggtgttaaggcgttttgtatttgatggctgctttctgataaagactagctctattttatgatttggtgttatcgatgttgatcgggattagttagtcccaaagttggagttaccaaccttctttcttagtttggtcactgtggtattcaacattttaagatctttctctatgtttcagAGACTGCACTAAAACTTGACACTTTAGTTGGTGATATTGAGGATGCTGTGATGTCTTCTTTGAATAAAAACTTAAGAA--CAT-CTCGGTCAAGTGGTTTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaaactttccacttctttttttttctctccctatcgtttttgcgattctttcagAGACAGCATTAAAACTTGACAGTTTGGTTGGTGACATCGAAGATGCTGTATCTTCTACTATGAACAGAAATCTAAAGAAGCATGCTTCCACACACAGTTC
gactaaa putative branch site (score: 2)
cttctttttttttctc putative PPT
acttcttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttacaagttattgcaatgcctattactgttaattctgatagtgactaaactttccacttctttttttttctctccctatcgtttttgcgattctttcagAGACAGCATTAAAACTTGACAGTTTGGTTGGTGACATCGAAGATGCTGTATCTTCTACTATGAACAGAAATCTAAAGAAGCATGCTTCCACACACAGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - caatgcc
- - - - - - - - - - - - - - - - - -ctgatag