Sequence
atgc intronic sequence ATGC exonic sequencegtatctaccattgtgttgttcggtctcaattttatactatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 9
gtatctaccattgtgttgttcggtctcaattttatactatattttggattatttttgaggtctaattactttg-----agtgatt--ttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
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------------------------gtaaattcaaaagcccttctagaattaattttagagtgggcacactttgcttatgatgattactgttatctttatattctagATTGTCCTGGAAGCCGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGTTTAAAATCCTTAATAAAAGGAGTACTTGAAATGGCAAAGGAGCCAT
upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
gtatctaccattgtgttgttcggtctcaatttta-tactatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
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----gtaagattggatc---cagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgac---attctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os08g32920.1 (Oryza sativa), 3'ss of exon 9
gtatctaccattgtgttgttcggtctcaattttatactatattttggattatttttgaggtc-taattactttgagtgattttcccccatttg----gtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
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------gtaattcggttattc---ttgaagcttctgttacttgactcatcaattgtatggttataatcaatagatattccttttgcctttttcttttgtgccagATTGTTCTTGAGGCTGATGGTTACCAACCATACCTGATATCACCTGAAAAAGGTTTAAGATCTCTTATAAAAGGTCTTCTAGAATTAGCAAAGGAACCAT
upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
gtatctaccattgtgttgttcggtctcaattttatactatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
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------------gtat-gatcacttccaattttacattgagctctggttggcagttagcacatgatta----aacacatttctctccacacaat---agATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 9
gtatctaccattgtgttgttcggtctcaattttatactatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
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gtaagttttgaaccactgatccgttgatatctttt------ttttgcctagggtgggggatgctattactcttgcttacccttttt-gtctgttaccagATTGTGTTAGAAGCAGATGGTTATCAGCCTTATCTTATTTCCCCTGAAAAGGGATTGAGATCTCTAATCAAAGGTGTTCTAGAGCTTGCGAAAGAGCCGT
upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G00430.1 (Glycine max), 3'ss of exon 9
gtatctaccattgtgttgttcggtctcaattttatactatattttg--gattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
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------------------------gtaagttttgaaccactgtttgttgatatcttttttggtt--attactct---tgcttaccctttgtctcttatcagATTGTGTTAGAAGCAGATGGTTATCAGCCGTATCTTATTTCCCCTGAAAAGGGATTGAGATCTCTAATCAAAGGGGTTCTAGAGCTTGCGAAAGAGCCAT
upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatctaccattgtgttgttcggtctcaa-ttttatac-tatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
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--gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgaca-----gattgattttcca--att--gtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatctaccattgtgttgttcggtctcaattttatactatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
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------gtgggtgtcttcttctgtcctaagtttctgcacga-----gacaagttttgagacttgatttgtcaaaatatctttg----atttt----cagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGGMapped 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|161717164|gb|FC065927.1|FC065927EST: TCAAGCAGCTCCCTTTAGACAGGCATTTTGACATCAACAATGTCAAAAGG ATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAA
genomic: TCAAGCAGCTCCCTTTAGACAGGCATTTTGACATCAACAATGTCAAAAGGgtatctacca ... ttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
gtctaat putative branch site (score: 3)
ttttcccccattt putative PPT
taattacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctaccattgtgttgttcggtctcaattttatactatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT