Sequence
atgc intronic sequence ATGC exonic sequence...tctgtttgaattttgactcttctatttagtgtttcagaattttataattttaattttgcctctaaacttctgatattactctcttggttttgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g07310.3 (Oryza sativa), 3'ss of exon 3
---tctgtttgaattttgactcttctatttagtgtttcagaattttataattttaattttgcctctaaacttctgatattactctct-tggttttgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAG
|| ||| || ||| | | ||| | || || | | | ||| | || | || || | || || | || || ||||||||||| |||||||| |||||||| |||||| | || || || |||||||| ||||||| || ||
taaacttattgcatgttgtgagatgcagttatcactcca---ccttgcacactaaccactgcacc-aaggtcatgctaaaatgctgaatgctctttgttttcagATGACAAAGCTGGCAATTATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG
upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 3
-tctgtttgaatttt-----gactcttctatttagtgtttcagaattttataattttaattttgcctctaaacttctgatattactctcttggttttgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAG
||||| || || ||| ||||| | || | || | | | | ||||| || | | || | | | || || || | | | ||||||||||| ||||| || || |||||||||||| | ||||| ||||||||||| ||||||| ||| ||
cattgtttatatgttcagatgacaacgctattca-tgccactccatctcaca-tgctaattactccaccaggctcataacaaaacactgtttatatg----ttcagATGACAAAGCTGGCTATTATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCAGGAAGAAATTTAG
upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 3
---------tctgtttgaattttgactcttctatttagtgtttcagaattttataattttaattttgcctctaaacttctgatattactctcttggttttgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAG
| || || | |||||| || ||||| ||| | || | | | | ||||| || | | || | | | | || || | | | ||||||||||| ||||| || || |||||||||||| | ||||| ||||||||||| |||||| ||| ||
gtacaaccatatggtttcaatttgacgct---attta-tgtcactacatctcaca-tgctaattactccaccatgctcataacaaaatactgtttatatg----ttcagATGACAAAGCTGGCCATAATTCCCTGTACTGTTATACTGGAGACCCTTTTCTTCCGGAAGAAATTTAG
upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 4
-------tctgtttgaattttgactcttctatttagtgtttcagaattttataattttaattttgcctctaaacttctgatattactctcttggttttgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAG
|| || |||| ||||| | |||| |||| | ||| | | | || | ||| | | ||| | || |||||||||||||| ||||||||||||||||||||| | | || ||| | ||||| || |||| |||||
gtacaacccttatttcttttttgtcgttctagctgctgtt---gaatgtgata-tcgtgttcttaacctcgttcttgtatacatgtcttctcttcccttgatatcagATGACAAAACTTGCAATCATCCCCTGTACTGTTGTCTTAGAGACCATCTTCTTCAGAAAGATGTTCAG
upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 3
tctgtttgaattttgactcttctatttagtgtttca-gaattttataattttaatt--ttgcctctaaacttctgatattactctcttggttttgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAG
|| | |||| | ||| | ||| || | | | | | | |||||| | | | || |||| | || | ||| || ||||||| ||||| || ||||||||||| |||||||| |||| ||||| ||||| ||||| | |||||
---gtatagctttttccatttc-agttactgcatgatgtgatatccatttttaactagtgttgttctaatttctaacccatcttctgttccgttg-ataatagATGACTAAACTAGCTATCATCCCCTGCACTGTTCTCTTGGAGACCCTCTTCTTCAGGAAAAAGTTCAGMapped 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|110699675|gb|EE076891.1|EE076891EST: TTGGGCTTTTGAATCTTAGCTTGGGTTTCAATTCTGTTGGTTTCTACCAG ATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTC
genomic: TTGGGCTTTTGAATCTTAGCTTGGGTTTCAATTCTGTTGGTTTCTACCAGgtacattttt ... tgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTC
EST:
gi|110699527|gb|EE076603.1|EE076603EST: TTGGGCTTTTGAATCTTAGCTTGGGTTTCAATTCTGTTGGTTTCTACCAG ATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTC
genomic: TTGGGCTTTTGAATCTTAGCTTGGGTTTCAATTCTGTTGGTTTCTACCAGgtacattttt ... tgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttaattttgcctctaaacttctgatattactctcttggttttgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAG
ttctgat putative branch site (score: 3)
taatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgtttgaattttgactcttctatttagtgtttcagaattttataattttaattttgcctctaaacttctgatattactctcttggttttgcattccagATGACAAAACTGGCAATCATCCCCTGTACTGTTCTTCTGGAAACCCTTTTCTTTAGGAAGAGATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
-ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcttgg