Sequence
atgc intronic sequence ATGC exonic sequence...tgtatgtgtttgggcttgctgacgtgtagtttggtgtatattattgctcatcattatattctttcctttttgctcatggaactgtgtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC195874.2_FGT002 (Zea mays), 3'ss of exon 4
---------tgtatgtgtttgggcttgctgacgtgtagtttggtgtatattattgctcatcattatattctttcctttttgctcatggaactgtgtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG
| || || || | | || | | || ||| | | || || || || | | | | ||||| || | |||||||| || ||||| || ||||| ||||||||||||||||| ||||||||||||||||||
taaaaaccaaacacgtagttacgcctttta---tgaacctctgtctatgatgctatcaatagttgtaaaattag----tgatccttatttttctgtttacct--tgaagGTTTACCTGATACTAGATGAATTTATTCTTGCTGGGGAGCTGCAAGAAACAAGCAAAAAG
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G052713_T01 (Zea mays), 3'ss of exon 4
tgtatgtgtttgggcttgctgacgtgtagtttggtgtatattattgctcatcattatattctttccttt----ttgctcatggaactgt-gtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG
|| || ||| | | | | | | || | || | || | | | | | ||||| || || || | | | |||| | ||||||| | ||| | || || |||||||||||||| ||||| |||||||||||||||| |
-----ctgcttttgctctttaatcttttgccttccttaaaccatactaaagtatctaactatcatttgtgaatttgcttattgatcttttggctatctgctgtagGTTTACTTGATATTGGATGAGTTCATTCTTGCTGGAGAGCTTCAAGAAACAAGCAAAAGG
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 4
tgtatgtgtttgggcttgctga-cgtgtagt-ttggtgtatattattgctcatcattatattctttcctttttgctcatggaact-gtgtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG
|| | | | ||| ||| | || | || |||||| | | ||| | || | | || ||||| | | | | | | ||||| |||||||||||||| ||||||||||| || || || || |||||||||||||| |||
--gatcaccattaccatattgatcgtaccctcttcctttagattattatt-actatttttttaatgtttccttactcatatagtttacccatatgtcttgaagGTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACAAGCAAGAAG
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G37730.1 (Glycine max), 3'ss of exon 4
-tgtatgt-gtttgggcttgctgacgtgtagtttggtgtatattattgctcatcattatattctttcctttttgctcatggaactgtgtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG-
|| ||| | | | | | | || | ||||||| || | || || | ||||||| | | | | | ||||| | ||||| |||||||||||||| ||||||||||| || || || || |||||||||||||| |||
ccaagtgaagttcatgatcgtaatcctctttcttaagat-tattattactatttcttttaatgtttccttactcatttagtttacctatatgtct--tcaaggTCTATCTTATACTTGATGAATTCATTCTAGCGGGTGAACTGCAAGAAACAAGCAAGAAGG
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 4
tgtatgtgtttgggcttgctgacg-tgtagtttggtgtatattattgctcatcattatattctttcctttttgctca-tggaactgtgtttgtctgat--aaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG
| | ||||||| ||| || | | ||| || | || ||| || || | | || | | ||||| | | | | | | | | |||||| || | ||||| || || ||||||||||||||||||||||||||||||||||||| |
tatttgtgtttatatatgcagatgctacagt---gtttctagatttgatctgtgtt-tgtactctaataattgctaactagttccctatgacttaaactgaaagGTGTACTTGATACTCGATGAGTTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAGG
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ09792 (Selaginella moellendorffii), 3'ss of exon 4
tgtatgtgtttgggcttgctgacgtgtagtttggtgtatattattgctcatcattatattctttcctttttgctcatggaactgtgtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG
|| | | | | | | | | | | | | || | | || | || ||| || || || ||||||| | || || ||||| |||||||||||||| ||| | |||||||| |||||||||
-----------------gccagtttctttccttgcttttttattctcccggtctggtgttgcaagcactcagcgcctg---ctggtttcgtt---tacagGTTTACTTGATCCTCGACGAGTTCATTCTTGCTGGCGAGTTACAAGAAACCAGCAAAAAG
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ11600 (Selaginella moellendorffii), 3'ss of exon 4
tgtatgtgtttgggcttgctgacgtgtagtttggtgtatattattgctcatcattatattctttcctttttgctcatggaactgtgtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG
|| | | | | | | | | | | | | || | | || | || | | || || || ||||||| | || || ||||| |||||||||||||| ||| | |||||||| |||||||||
-----------------gccagtttctttccttgcttttttattctcccggtctggtgttgcaagcactcagcgcctg---ccggtttcgtt---tacagGTTTACTTGATCCTCGACGAGTTCATTCTTGCTGGCGAGTTACAAGAAACCAGCAAAAAGMapped 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|37188193|gb|CF607542.1|CF607542EST: ATTTCTTCAGCAATGTGTGCGAGCTAGATTTGGTATTTAATTTCCACAAG GTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACA
genomic: ATTTCTTCAGCAATGTGTGCGAGCTAGATTTGGTATTTAATTTCCACAAGgtttgttact ... tctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcatcattatattctttcctttttgctcatggaactgtgtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG
gtctgat putative branch site (score: 4)
tttgtct CT-rich tract
tcattatattcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtatgtgtttgggcttgctgacgtgtagtttggtgtatattattgctcatcattatattctttcctttttgctcatggaactgtgtttgtctgataaagGTTTATCTTATACTTGACGAATTCATTCTTGCTGGGGAGCTCCAAGAAACAAGCAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
-gtatgtg
- - - - - - -gcttgct
- - - - - - - - - - - - - - - -tggtgta
- - - - - - - - - - - - - - - - - - - - - - - ctcatca