Sequence
atgc intronic sequence ATGC exonic sequencegtagagtgctgtttgacattatttgacttttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g00700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g46020.1 (Oryza sativa), 3'ss of exon 2
gtagagtgctgtttgacattatttgacttttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTC
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gtaaaaggata---agatttgtttaagatctgttttat--caattgtaggcttttaagaatcttacattgagtt--tgtaacagATGATTATGGTAAGAGAAGAAGATGATCCTGCTCCAGAAGGAATTGAATACACACATGGTCTTACTCCTCCAATGAGGGATGCACGAAGGCGGCGTTTCC
upper sequence: Vv06s0004g00700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 2
gtagagtgctgtttgacattatttgacttttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTC
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gtaaagcataggtt--ttgtgtataagatctgttttattaactgtaggcttttaagactctcctgttgaga----ttataacagATGATTATGGTAAGAGAAGAAGAAGATCCTGCTCCAGAAGGAGTTGAATACAAGCATGGTCTTACTCCTCCAATGAGGGACGCACGCAGGCGGCGTTTCC
upper sequence: Vv06s0004g00700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G46640.1 (Glycine max), 3'ss of exon 2
------gtagagtgctgtttgacattatttgacttttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTC
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gtcagattcaaataattcttt-cattcttaatcatactctttgattcatataacgttctaactggttactgcatccaact-----aacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTACAGACATGGCCTCACTCCACCCATGAGAGATGCTCGCAAGCGTAGATTTC
upper sequence: Vv06s0004g00700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G17970.1 (Glycine max), 3'ss of exon 1
gtagagtgctgtttgacattatttgacttttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTC
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-----gt-cagattcaaataattc-attcattcttaatcatactctttgattcatataactgcttactgcatccaac-taacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTTATTGAGTACAGACATGGCCTCACTCCACCCATGAGAGATGCTCGCAAGCGTAGATTTC
upper sequence: Vv06s0004g00700.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G24450.1 (Glycine max), 3'ss of exon 2
------gtagagtgctgtttgacattatttgacttttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTC
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gtcagattcaaataattcttt-cattcttaatcatactctttgattcatataacgttctaactggttactgcatccaaca-----aacagATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTACAGACATGGCCTCACTCCACCCATGAGAGATGCTCGCAAGCGTAGATTTCMapped 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|30253284|gb|CB970835.1|CB970835EST: ACAAAACTTATGACGATAGTGTGCTAATCAAAACTGCTGACATT-G---- ATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTAT
genomic: ACAAAACTTATGACGATAGTGTGCTAATCAAAACTGCTGACATTGGTCAAgtagagtgct ... gttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTC
tactaat putative branch site (score: 1)
attactaat 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
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gtagagtgctgtttgacattatttgacttttttttttttacagttaagtgattgcttcattactaatgcaagttgttataacagATGATTATGGTGCGAGAAGAAGGTGATACTGCTCCAGATGTGGTGGAGTATCGACATGGCCTCACTCCTCCAATGAGGGATGCCCGAAAGCGAAGATTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA