Sequence
atgc intronic sequence ATGC exonic sequence...aaataaaattatctgatgtggactgaaaatagaggtcttaattgtgttttttcgtattaagcacctaggctcttacaatcttgttggatgtttaaaacagGTTGCTGATTTTGGGCTTTCGAGGGAAGAGATGGTTAGCAAACATGCATCTAATATACGAGGAACTTTTGGATATCTTGATCCTGAGTATGTATCAACAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0014g04960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os08g04420.1 (Oryza sativa), 3'ss of exon 5
aaataaaattatctgatgtggactgaaaatagaggtcttaattgtgttttttcgtattaagcacctaggctcttacaatcttgttggatgttta--aaacagGTTGCTGATTTTGGGCTTTCGAGGGAAGAGATGGTTAGCAAACATGCATCTAATATACGAGGAACTTTTGGATATCTTGATCCTGAGTATGTATCAACAA
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--gtagttcaaaatacagtacttcttggataacactggatatggtgtcttattgtactaaaatgttttattctcagactaatgagcactttctgttggccagGTTGCAGACTTTGGATTATCAAGAGAAGAAATGGTTACTCGAAATGGAGCCAACATACGTGGAACTTATGGATATCTTGATCCAGAGTATGTGTCCTCAC
upper sequence: Vv19s0014g04960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G41510.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------aaataaaattatctg-atgtggactgaaaatag-aggtcttaatt-gtgttttt----tcgtattaagcacctaggct-cttacaatcttgttg--gatgtttaa---aacagGTTGCTGATTTTGGGCTTTCGAGGGAAGAGATGGTTAGCAAACATGCATCTAATATACGAGGAACTTTTGGATATCTTGATCCTGAGTATGTATCAACAA---
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gtatgatgatactcatccctcatatttcatcacaaaaagtagtttgcaccaaatatacacacccctatacaaagctaaattactaactattcattagtgttgtcataatcatttattgcttttaggatgcttcttattctgtagttaatgttgaatcaagcagGTTGCTGATTTTGGACTTTCAAGAGAAGAGATGGTGGATAAACATGCAGCTATT---CGGGGTACCTTTGGCTATCTTGACCCCGAGTATATATCTTCCGGAA
upper sequence: Vv19s0014g04960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G16650.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------aaataaaattatctgatgtggac-tgaaaatagaggtct-taattgtgttttttcgtattaagcacctaggctcttacaatcttgttgg--atgtt---taaaacagGTTGCTGATTTTGGGCTTTCGAGGGAAGAGATGGTTAGCAAACATGCATCTAATATACGAGGAACTTTTGGATATCTTGATCCTGAGTATGTATCAACAA---
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gtatgtccttgttactcgtccatcatctttatcacgaaaagtagctagcaataaatactcacactatacattagtttattttg-gtgaatgtcacaatacattactgttgtcatagtcatttgttgctgttaggatgcttcttaatctttaggtgataatgttggatcaatcagGTTGCTGATTTTGGACTTTCAAGAGAAGAGATGGCGAATAAGCATGCAGCTATT---CGGGGTACCTTTGGCTATCTTGACCCCGAGTATATATCTTCAGGAA
upper sequence: Vv19s0014g04960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G36140.2 (Glycine max), 3'ss of exon 6
----aaataaaattatctgatgtggactgaaaatagaggtcttaattgtgttttttcgtattaagcacctaggctcttacaatcttgttg--gatgtttaaaacagGTTGCTGATTTTGGGCTTTCGAGGGAAGAGATGGTTAGCAAACATGCATCTAATATACGAGGAACTTTTGGATATCTTGATCCTGAGTATGTATCAACAA---
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tgtctagtgatattgcttaatg---attatgtctatttcttttagtcatttagtgttggttaggatgctt---cttacacataattgttgatgctgaatcaaacagGTTGCTGATTTTGGACTCTCAAGAGAAGAGATGGTGGATAAACATGC---TGCAATTCGGGGTACCTTTGGCTATCTTGACCCTGAGTATATATCCTCAGGGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|161713605|gb|FC063415.1|FC063415EST: GGGACATCAAATCATCCAATATTCTATTGGACCAGTCCATGAGAGCAAGG GTTGCTGATTTTGGGCTTTCGAGGGAAGAGATGGTTAGCAAACATGCATCT
genomic: GGGACATCAAATCATCCAATATTCTATTGGACCAGTCCATGAGAGCAAGGgtatgcctca ... tttaaaacagGTTGCTGATTTTGGGCTTTCGAGGGAAGAGATGGTTAGCAAACATGCATCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttttcgtattaagcacctaggctcttacaatcttgttggatgtttaaaacagGTTGCTGATTTTGGGCTTTCGAGGGAAGAGATGGTTAGCAAACATGCATCTAATATACGAGGAACTTTTGGATATCTTGATCCTGAGTATGTATCAACAA
ctcttac putative branch site (score: 3)
atgtttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaataaaattatctgatgtggactgaaaatagaggtcttaattgtgttttttcgtattaagcacctaggctcttacaatcttgttggatgtttaaaacagGTTGCTGATTTTGGGCTTTCGAGGGAAGAGATGGTTAGCAAACATGCATCTAATATACGAGGAACTTTTGGATATCTTGATCCTGAGTATGTATCAACAA
aaataaa
- - - - - - ctgatgt
- - - - - - - - - - - - gaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttg