Sequence
atgc intronic sequence ATGC exonic sequence...ggaagcttgcaatattttacctactgtgattatcattattattattattgtgtgtactgatgcatgtttttgttggtgactgtttgaattacctttacagTCTACCCGTTGGCTACTTTACACCGAACAAGCACCTTCTGCTTGGATGAACTTTGCCTTATGTGGATTAGTTGGAATTATGACAGCTTATGTTTTTGTCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 9
--ggaagcttgcaatattttacctactgtgattatcattattattattattgtgtgtactgatgcatgtttttgttggtgactgtttgaattacctttacagTCTACCCGTTGGCTACTTTACACCGAACAAGCACCTTCTGCTTGGATGAACTTTGCCTTATGTGGATTAGTTGGAATTATGACAGCTTATGTTTTTGTCT
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ggttatgttggtgttgtcttgttcttccttttctgcagta--aacatcaaattcttttttctctgaagtttgttataataattggcctgtgtacattttcagTCTACCCGGTGGCTCCTGTACACTGAACAAGCACCTTCTGCATGGCTCAATTTTGCCTTGTGTGGCTTGGTGGGCATCATCACAGCATATGCTTTTGTTT
upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G069410_T01 (Zea mays), 3'ss of exon 1
ggaagcttgcaatatttta--cctactgtgattatcattattattattattgtgtgtactgatgcatgttt-ttgttggtgactgtttgaattacctttacagTCTACCCGTTGGCTACTTTACACCGAACAAGCACCTTCTGCTTGGATGAACTTTGCCTTATGTGGATTAGTTGGAATTATGACAGCTTATGTTTTTGTCT
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atgtgtttgtgatgtcttgtgtcttcccttatacaaagtaaaatcatacctttctccccagaagttgatttcttgttattga---tttgtgttaaattttcagTCTACTCGTTGGCTTCTGTACACGGAACAAGCACCTTCTGCATGGCTGAATTTTGCATTGTGTGGCTTGGTGGGGATCGTCACAGCATATGCTTTTGTTT
upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 9
-ggaagcttgcaatattttacctactgtgattatcattattattattattgtgtgtactgatgcatgtttttgttggtgactgtttgaattacctttacagTCTACCCGTTGGCTACTTTACACCGAACAAGCACCTTCTGCTTGGATGAACTTTGCCTTATGTGGATTAGTTGGAATTATGACAGCTTATGTTTTTGTCT
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tctgtgtttgtgatgtcttgtcttccctttatacaaagtaaaatcatacctttctcaccagaagttgattt-attattattgatctgtgttgaatttccagTCTACTCGTTGGCTCCTGTACACGGAACAAGCACCTTCTGCATGGCTAAATTTTGCATTGTGTGGCTTGGTGGGGATCATCACAGCATATGCTTTTGTTT
upper sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 9
------------ggaagcttgcaatattttacctactgtgattatcattattattattattgtgtgtactgatgcatgtttttgttggtg-actgtttgaattac----ctttacagTCTACCCGTTGGCTACTTTACACCGAACAAGCACCTTCTGCTTGGATGAACTTTGCCTTATGTGGATTAGTTGGAATTATGACAGCTTATGTTTTTGTCT
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gtaatatttaatcttcttttgtgatatttta---attttgcttttctatactctctggattg-gtcaaccattcaccgttccaattgctgtaatttttaaattgaattactttgcagTCTACCCGGTGGTTACTTTACACTGAGCAAGCACCTTCAGCATGGTTCAATTTTGCTTTGTGTGGGTTGATTGGTATTATCACTGCTTACATATTTGTCTMapped 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|77580819|gb|DV219323.1|DV219323EST: AGAAAGGATACTCCATTACAATAATTTTAGCTGTTTTGACATTTGGCTTG TCTACCCGTTGGCTACTTTACACCGAACAAGCACCTTCTGCTTGGATGAAC
genomic: AGAAAGGATACTCCATTACAATAATTTTAGCTGTTTTGACATTTGGCTTGgtaagatttc ... acctttacagTCTACCCGTTGGCTACTTTACACCGAACAAGCACCTTCTGCTTGGATGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgtgtgtactgatgcatgtttttgttggtgactgtttgaattacctttacagTCTACCCGTTGGCTACTTTACACCGAACAAGCACCTTCTGCTTGGATGAACTTTGCCTTATGTGGATTAGTTGGAATTATGACAGCTTATGTTTTTGTCT
tactgat putative branch site (score: 2)
ttaccttt putative PPT
tttgaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaagcttgcaatattttacctactgtgattatcattattattattattgtgtgtactgatgcatgtttttgttggtgactgtttgaattacctttacagTCTACCCGTTGGCTACTTTACACCGAACAAGCACCTTCTGCTTGGATGAACTTTGCCTTATGTGGATTAGTTGGAATTATGACAGCTTATGTTTTTGTCT
- - gcttgca
- - - - - - - - - -cctactg
- - - - - - - - - - - - - - - - - - - - - - - - tgtgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgactgt