Sequence
atgc intronic sequence ATGC exonic sequence...gtatcaaatgcatgcatgtgcatacaaacattctgcatatcatatccactggctatatatctgatctgacatgctcatgcctatctgttttgggttttagGTGGGCTGCAGCTGCCGGACAGGTTTCACTCAATGGAATGATTCTTCCTGCTGCCCTCTATTTTTGGCAAATACCCCATTTTATGGCCCTAGCATACTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0021g00430.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g34390.1 (Oryza sativa), 3'ss of exon 4
--------gtatcaaatgcatgcatgt-gcatacaaacattctgcatatcatatccactggctatatatctgatctgacatgctcatgcctatctgttttgggttttagGTGGGCTGCAGCTGCCGGACAGGTTTCACTCAATGGAATGATTCTTCCTGCTGCCCTCTATTTTTGGCAAATACCCCATTTTATGGCCCTAGCATACTTG
|| |||| | | ||| | || | || | | | | |||| || | | |||||| | | || | |||| || | | |||||||| |||||| | | | ||||| |||| |||||||| |||||||| | || | |||||||||||| |||||||||||||| ||||||||
atcagtatgtgtcaatgtcctatctgttgaatgccaatgagggacctttttt-tccattgcc-----acatgatctca-gtccttaatttcatcttcttctg--tacagGTGGGCAGCAGCTTCGTCTGAACTGTCACTGAATGCTATGATTCTCCCTGCTGCATTGTACTATTGGCAAATACCACATTTTATGGCCCTTGCATACTTA
upper sequence: Vv15s0021g00430.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 4
gtatcaaatgcatgcatgtgcatacaaacattctgcatatcatatccactggctatatatctgatctgacatgctcatg-cctatctgtt-ttgggttttagGTGGGCTGCAGCTGCCGGACAGGTTTCACTCAATGGAATGATTCTTCCTGCTGCCCTCTATTTTTGGCAAATACCCCATTTTATGGCCCTAGCATACTTG
| || | | | | ||| || || | | | || ||| | || | | | | ||||| ||| | |||| ||| ||| || |||||||||||| | | ||||||| ||||||||||||||||| ||||| | ||||||||||||||||| ||||||||||||||||| || |||
-tctctcttttttctttttctttactcacgttgt-ctcacttcattcaccatgtgtacgtgtattttctgcccctcatctcctttttgttgttgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGCTGCTTTGTATTTTTGGCAAATACCACATTTTATGGCCCTAGCCTATTTG
upper sequence: Vv15s0021g00430.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G43980.1 (Glycine max), 3'ss of exon 6
gtatcaaatgcatgc-atgtgcatacaaacattctgcatatcatatccactggctatatatctgatctgacatgctcatgc--ctatctgttttgggttttagGTGGGCTGCAGCTGCCGGACAGGTTTCACTCAATGGAATGATTCTTCCTGCTGCCCTCTATTTTTGGCAAATACCCCATTTTATGGCCCTAGCATACTTG
| | |||| | | | || || || | | ||| || || | | | | | || | | || | || | | | ||| ||| || |||||||||||| | | ||||||| |||| |||||||||||| | ||| | ||||||||| ||||||| || ||||||||| |||| || |||
-ttctttactcatgttgtctcacttcattcaccatgtgtgt-ataggcatgtgc-acgtgtattttttgcccttcttcaccttctttttatgttgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGCAATGATTCTTCCAGTTGCTTTGTATTTTTGGAAAATACCACACTTTATGGCCTTAGCCTATTTG
upper sequence: Vv15s0021g00430.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G44520.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------gtatcaaatgcatgcatgtgcatacaaacattctgcatatcatatccact---ggctatatatctgatctgacatgctcatgcctatctgttttgggtttt---agGTGGGCTGCAGCTGCCGGACAGGTTTCACTCAATGGAATGATTCTTCCTGCTGCCCTCTATTTTTGGCAAATACCCCATTTTATGGCCCTAGCATACTTG
| || | || | || | | || ||| | | | | || || | || |||| ||||| ||||| || || |||||||| ||||| | || ||| ||||| |||| ||||||||||| ||||| || || |||||||| ||||| |||||||||||||| ||| | |
gtaaatttttgttccttttcttctttattttagcagattctgttttgttggatactgcttttaattcaaaatgtagtcatggttcaccaattctatgcttatctattttgtgtgttgtcagGTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGCTGCTCTTTACTTTTGGCAGATACCTCATTTTATGGCCCTTGCACATCTCMapped 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|22014827|gb|BQ799861.1|BQ799861EST: GTTG-TGGTGCTATTCCGCCACTGCTTGG GT-GGCTGCAGCTGCCGGACAGG-TTCACTCAATGGAATGA-TCTTCCTGC
genomic: GTTGTTGGTGCTATTCCGCCACTGCTTGGgtaatttttt ... tgggttttagGTGGGCTGCAGCTGCCGGACAGGTTTCACTCAATGGAATGATTCTTCCTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccactggctatatatctgatctgacatgctcatgcctatctgttttgggttttagGTGGGCTGCAGCTGCCGGACAGGTTTCACTCAATGGAATGATTCTTCCTGCTGCCCTCTATTTTTGGCAAATACCCCATTTTATGGCCCTAGCATACTTG
atctgac putative branch site (score: 3)
tctgtttt putative PPT
tatatatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcaaatgcatgcatgtgcatacaaacattctgcatatcatatccactggctatatatctgatctgacatgctcatgcctatctgttttgggttttagGTGGGCTGCAGCTGCCGGACAGGTTTCACTCAATGGAATGATTCTTCCTGCTGCCCTCTATTTTTGGCAAATACCCCATTTTATGGCCCTAGCATACTTG
- atcaaat
- - - - -gcatgca
- - - - - - - - - -gcataca
- - - - - - - - - - - - - - - - ctgcata
- - - - - - - - - - - - - - - - - - - - - - tccactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgctc