Sequence
atgc intronic sequence ATGC exonic sequence...atgcgctattttgttaattgtcttgaatattatttatttgtgtttgtgatcaaaacttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g63750.1 (Oryza sativa), 3'ss of exon 1
---atgcgctattttgttaattgt-cttgaatattatttatttg-tgt-ttgtgatcaaaacttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
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atcatataacactcagtcagaagtacttgtaccgggcagatacactgtgccatgtacgttagccggcctctaacg---atctcattggtgcactta---tgagcagGGATTTAGGAAAGTTGATCCAGATAGGTGGGAGTTTGCAAACGAAGGTTTTCTTAGAGGACAAAAGCATCTACTGAAGACCATCAACAGAAGGAAACCAA
upper sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G384339_T02 (Zea mays), 3'ss of exon 2
--atgcgctattttgttaattgtcttgaatattatttatttgtgtttgtgatcaaaacttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
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ccttaatttgatttgcactcagctgacaatcgggagagattattttctcagctaacaattatattgcgccctaacgatctcatcggtgccttctt--accagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAAAAACATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G115456_T01 (Zea mays), 3'ss of exon 1
atgcgctattttgttaattgtcttgaatattatttatttgtgtttg-tgatcaaa--acttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
| ||| | | | | | || ||| | | ||| | | |||| | ||| || | | | | ||| | || | | ||||| ||||| ||||| ||||||||| | |||||||||||||||||||||||||| ||||| || || || || |||||| ||| | || | ||| |
-tcacatatgatctgcactctactggcaattggaagatgctattttctcagcaaacaatttatattgcaccctaacgatgtcatctgtgcctt--tttaccagGGGTTTAGAAAGGTTGATCCAGACAGATGGGAATTTGCAAATGAGGGTTTTCTGAGAGGACAGAAGCATCTGCTGAAGACTATCAACAGAAGGAAACCAT
upper sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G01190.1 (Glycine max), 3'ss of exon 1
atgcgctattttgttaattgtcttgaatattatttatttgtgtttgtgatcaaa---acttagtttctaaggggtagtttttttcttcactttaat--caaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
||| | ||| || | | |||| | || || || | | || | ||| || ||| || || | || | | ||||||||| || || ||||| || ||||| || ||||||||||||||||| || ||| |||||||| ||||||| ||||| || ||||| |||||||| |||||
-----gcattattagcattacatttagttttatcaagctggattagttgtacagttcacacatttttcttctcttaatttgttactccttttgattgacaaacagGGTTTCAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
upper sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G44330.1 (Glycine max), 3'ss of exon 1
----atgcgctattttgttaattgtcttgaatattatttatttgtgtttgtgatcaaaacttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
| ||| | | | | | || | ||| |||| | | | | || |||| ||| || | || || | ||| ||||| ||||| ||||| || ||||| || ||||||||||||||||| || ||| |||||||| ||||||| ||||| || ||||| |||||||| |||||
gcataattaacattacatgtagttttatcaagctggattagttgtacaattcac--acatttctcttctcttaatctgttattctttttgattga--caagcagGGTTTTAGAAAGGTTGACCCAGATCGATGGGAATTTGCAAATGAAGGATTTTTAAGAGGTGAAAAACAACTTTTAAAAAGTATCAGTAGGCGGAAATCTG
upper sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G02990.1 (Arabidopsis thaliana), 3'ss of exon 1
atgcgctattt-tgttaattgtcttgaatattatttatttgtgtttgtgatcaa--aacttagt-ttctaaggggtagtttttttcttca--ctttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
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------tgtttatacaaatcttctatgttggcttcctattgcaacggaatccaagtaacttcttgcggttgatgactgttccattctccatgcttctttttttcagGGTTTTAGAAAAGTTGATCCAGACCGCTGGGAGTTTGCAAACGAGGGCTTTTTAAGAGGCCAAAAGCAAATACTAAAGAGTATTGTCCGGCGAAAACCTG
upper sequence: Vv16s0039g01840.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G16820.2 (Arabidopsis thaliana), 3'ss of exon 1
-atgcgctattttgttaattgt---cttgaatattatttatttgtgtttgtgatcaaaacttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
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tgttggcttttcttcttcccctaaattcaagcaacatcgtttcagttcttcaatttgaatttcgatatttatga-tagcctctctgt--attctgat-gtccagGGTTTCAGAAAAGTTGATCCTGACCGATGGGAATTTGCAAATGAAGGATTTCTTAGAGGCCGAAAACAACTACTGAAGAGTATTGTCAGGAGAAAACCTTMapped 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|294965443|gb|GW839014.1|GW839014EST: ACTTCAAGCACAATAATTTCTCCAGCTTTGTGAGGCAGTTGAATACTTAT GGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTT
genomic: ACTTCAAGCACAATAATTTCTCCAGCTTTGTGAGGCAGTTGAATACTTATgtgagtgttt ... aatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgatcaaaacttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
ctttaat putative branch site (score: 4)
tttttttcttcacttt CT-rich tract
tagttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgcgctattttgttaattgtcttgaatattatttatttgtgtttgtgatcaaaacttagtttctaaggggtagtttttttcttcactttaatcaaacagGGATTTAGGAAGGTGGATCCAGACCGCTGGGAATTTGCAAATGAGGGTTTTCTAAGAGGTCAAAAACACCTTTTGAAGAGTATTAGTAGGCGAAAATCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - atcaaaa