Sequence
atgc intronic sequence ATGC exonic sequence...ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G162881_T01 (Zea mays), 3'ss of exon 3
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
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---------------------------gtaggagtgcaatcatttattagattattttcttatcgaaatttctgtttttcacatgtaatctgatatgcagGTTTGTTGAAATAATGGCAACTGTATTCTCAAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
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gtaagtag--ctgctgatgtattta----tcatttacattatc---tagttt-aca--ggactgcatctcattgtgcta-tcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 10
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
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-------gtaa-gtagctgcttatg-tatttatcattacat-tatatagtct-acaa--gactgcatctcattgtgctagcactgttaatacaaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCGCGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G30850.1 (Glycine max), 3'ss of exon 8
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaa-atgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
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gtaagtaactgttaaagaatttttatttttttttggcaggggtacaatattttcccatcttt----aatgagctgatt--ccaccattctgtaacatgcagGTTTGTTGAGATAATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAG
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 8
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
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gtaagta--actgttacagattttttt--ttgggggggttacaatattttcccatctttagttag--------ctgattccaccattctgtaacatgcagGTTTGTTGAGATTATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAG
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 10
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
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---------------gtaagcatcagt-tgaagcattatttttgtattatccacccat---------accaaactgtatccaattatgttatgcatgcagATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCGTTGTGTCTGGCATATGATTCAG
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 10
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
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---------------gtaagcatcagt-tgaagcattatttttgtcttatctacccat---------accaaactgtatccaattatgttatgtatgcagATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCATTGTGTGTGGCATATGATTCAG
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttt-ccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG---------------------------------
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-------------------------gtacgtagtctcaaatgttcattacaaaaacatagatct-atacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 10
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
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gtatgtagaagcctttctttttacccgttttgagttggtttttccctataacaggaactaaccagtatcgaacttttgtgt----cattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G26440.4 (Arabidopsis thaliana), 3'ss of exon 10
ttgagcagtactgttgttattttttctgttcattcccact--cctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG---------------------------------
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-------gtatggatctcatttgtcaaaaccaatacaataagtattcatactctcttgatccatta------agttttgcacggttccttatc-------agGTTTATAGAGATTATGGCTCCAGTTTTCTCTAGAGAGGCATGGCGTTGTGTGTGGCATATGATTCAGAATGACTTGGTTCACGGTTGGGGTCTTGACTTT
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 9
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
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----gta-tgtttcaaaaaacgtctctatcaaactcaagtttcagacatatttaaacc--attagtaacttcgttat--gtctt--taataaaaaaacagATTCGTGGAGATAATGGCTCCTGTATTCTCAAGAGATGCATGGCGCTGCGTGTGGCATATGATCCAG
upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
--------ttgagcagtact--gttgttattttttctgttcattcccactcctgcatggt----ctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
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gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggt-atttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
gtctgac putative branch site (score: 3)
ttagttttccttttcc putative PPT
attagaaacaaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - ctgttgt
- - - - - - - - - - - - - - - - - cccactc
- - - - - - - - - - - - - - - - - - - - - - catggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - caatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
