Sequence
atgc intronic sequence ATGC exonic sequencegtactcctgttagtctaattgttcatcttcctgacattcttatcttttactcttgtttacatttgtgttgattttgtagttattgaatgcagagaaactaatacatattcacaatgtagGCTCTTCTTGCATATGGTCTGAGTAGCTCAAGGCGTGCTCCAGATGCTATCCACCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0054g00220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g23180.1 (Oryza sativa), 3'ss of exon 3
gtactcctgttagtctaattgttcatcttcctgacattcttatcttttactcttgtt-tacatttgtgttgattttgtagttattgaatgcagagaaactaatacatattcacaatgtagGCTCTTCTTGCATATGGTCTGAGTAGCTCAAGGCGTGCTCCAGATGCTATCCACCC
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---------------------------------gtagttgatgcttctacttttgctatctttttttgtaagctttgttgaaggttcatgtccagggcttaattgttgattaaacatcagGCTCTTCTTGCATATGGCTTGAGCAGCTCAAGACGTGCTCCAGATGCTCTACACCC
upper sequence: Vv09s0054g00220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G065839_T01 (Zea mays), 3'ss of exon 3
gtactcctgttagtctaattgttcatcttcctgacattcttatcttttactcttgtttacatttgtgttgattttgtagttattgaatgcagagaaactaatacatattcacaatgtagGCTCTTCTTGCATATGGTCTGAGTAGCTCAAGGCGTGCTCCAGATGCTATCCACCC
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----------------gtatgttttttttgctatgccagttgatgtttatacctttcctc-tctgtttcatgaccatgaataaagaactcagat---ctaattgttcatcaactttcagGCTCTTCTTGCTTATGGTTTGAGCAGCTCAAGACGTGCTCCAGATGCTCTACACCC
upper sequence: Vv09s0054g00220.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G51610.1 (Arabidopsis thaliana), 3'ss of exon 3
gtactcctgttagtctaattgttcatcttcctgacattcttatcttttactcttgtttacatttgtgttgattttgtagttattgaatgcag--agaaactaataca------tattcacaatgtagGCTCTTCTTGCATATGGTCTGAGTAGCTCAAGGCGTGCTCCAGATGCTATCCACCC
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--------------------gtttgt--tgctgttatgcttgtttgctgcttttgtgtccagtt----taatatattgactattgggtgcaggaaaaaactgatatatatatatattgatgttgtagGCACTTCTTGCTTATGGGCTCAGTAGCTCAAGGCGTGCCCCAGATGCTCTTCATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttgattttgtagttattgaatgcagagaaactaatacatattcacaatgtagGCTCTTCTTGCATATGGTCTGAGTAGCTCAAGGCGTGCTCCAGATGCTATCCACCC
aactaat putative branch site (score: 2)
aaactaatacatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcctgttagtctaattgttcatcttcctgacattcttatcttttactcttgtttacatttgtgttgattttgtagttattgaatgcagagaaactaatacatattcacaatgtagGCTCTTCTTGCATATGGTCTGAGTAGCTCAAGGCGTGCTCCAGATGCTATCCACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG