Sequence
atgc intronic sequence ATGC exonic sequence...ctaccaaagaacagatacaagtggtttccataatttactcttggatgtaagtttttatgtatggctttgatttgtaagtacggctttggctatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 4
ctaccaaagaacagatacaagtggtttccataatttactcttggatgtaagtttttatgtatggctttgatttgtaagtacggctttggctatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT
||| | | | ||||| |||| | ||| | | ||| | || | | | || ||| ||||||||||| ||||| || || || ||||| || || ||||| ||||| || ||||| |||||||| || || |||||||| ||||||||||| ||||| || |
----------------gtcagtt-ctgcagtcatttaagtaatgatgaatgttgctggactagagtttttgtactatg-atgtaattcattat-ttacagGTGGGCCTTCCAGGAACTGGAAAGACGCTTCTTGCAAAAGCTGTCGCAGGGGAAGCTGAAGTCCCATTCATAAGTTGCTCTGCAAGTGAATTTGTGGAGT
upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G37090.1 (Glycine max), 3'ss of exon 5
ctaccaaagaacagatacaagtggtttcca--taatttactcttggatgtaagtttttatgta---tggc-tttgatttgtaagtacggctttggctatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT
| | || | ||| | || |||| || || | | | || | || || | | | | |||| || | ||||||||||||||||||||||||||||||||||||| | || |||||||||||||| ||||| ||||| ||||| ||||||||||||||||| |||||||||||||| |
------cacagtgtatgtggattatttatagccaagttaccttttcatattattattgttttaatttgacatgtaggtagtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G39040.1 (Glycine max), 3'ss of exon 5
-ctaccaaagaacagatacaagtggtttccataatttactcttggatgtaagtttttatgtatggctttgatttgtaagtacggctttggctatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT
| | | || | | || ||| | || ||||| || | | | | | |||| || | ||||||||||||||||||||||||||||||||||||| | || |||||||||||||| ||||| ||||| ||||| ||||||||||||||||| |||||||||||||| |
ctcatcgtatgtggattatttatagccaagttactttttcatattattattgttttaatttgaaacgtaggta-gtaaatatccactgttttatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTTTACTGGCAAAGGCTGTGGCAGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTTGTAGAGT
upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA0028S00210.2 (Glycine max), 3'ss of exon 4
ctaccaaagaacagatacaagtggtttc----cataatttactcttggatgtaagtttttatgtatggctttgatttgtaagtacggct-ttggctatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT
|| || || || ||| || | || || ||||| || | | ||| | || || ||| || ||||||||||||||||||||| |||||||||||| | || |||||||||||||||||||| ||||| ||||| ||||||||||||||||| |||||||| |||||||
-----gaaatgttttcacttttgtctttgctgcatgtttgaggatttttaatattgttttaggttgacatctaggctgtgaatatctctcttgattaccttacagGTGGGTCTTCCTGGCACAGGTAAGACTTTACTTGCAAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT
upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 4
ctaccaaagaacagatacaagtggtttc--cataatttactcttggatgtaagtttttatgtatggctttgatttgtaagtacggctttggctatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT
| || | | || |||| ||| || | || | |||||| | | | | || | || ||| |||||||||||||||||||||||| |||||||||||| | || || ||||||||||||||||| ||||| ||||| ||||||||||||||||| |||||||| |||||||
-ttgaaatgttttcacttttgtcttttctgcatgtttgaggatttttaacattgttttatattgtcatctaggtagtgaatatc-tgttgattatcttacagGTGGGTCTTCCTGGAACAGGTAAGACTTTACTTGCGAAGGCTGTGGCTGGGGAAGCTGATGTGCCATTTATAAGTTGTTCTGCTAGTGAGTTCGTAGAAT
upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 4
----ctaccaaagaacagatacaagtggtttccataatttac-----tcttggatgtaagtttttatgtatg-gctttgatttgtaa--gtacggctttggct-----atcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT
| | | || | || ||| | || ||| | | |||| | | | ||| | ||| || || | ||||| || | || ||||| |||||||| || ||||| || || || || ||||||||||| |||||||| |||||||| || || |||||||| ||||||||||||||||||||
gtgagttttatcatttgatttcactttattcttatattacgtatatatcatggtttaacgtttggttacaagagctctcctttagaatgatatgcctttgactcctttcttttccagGTTGGTCTTCCCGGAACAGGGAAAACCCTTCTTGCAAAGGCTGTTGCTGGGGAAGCTGAAGTCCCCTTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGC
upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 4
----ctaccaaagaacagatacaagtggtttccataatttac---tcttggatgtaagtttttatgtatggctttgatttgtaagtacggctttggctatctta-cagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT
| | | || ||||| | | |||| ||| || | || ||| | | |||| | || | ||| || | || |||| ||||||||||| ||||| || || || || ||||| ||||| |||||||| |||| || || || |||||||| ||||||||||||||||||||
gtgagtttaataatgtagttacaacttatggccatttcttaggtggtttatgcgcaatgtttggttactatctttagaatttatggctttatttccctgttttggtagGTCGGTCTTCCTGGAACAGGGAAAACCCTTCTTGCAAAAGCTGTTGCTGGGGAATCTGATGTTCCATTCATAAGTTGCTCTGCAAGTGAGTTTGTAGAGCMapped 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|77579169|gb|DV218413.1|DV218413EST: CGGACAGGTATGTACGAGTTGGTGCTCGCCCTCCTCGAGGTGTTCTCCTG GTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGG
genomic: CGGACAGGTATGTACGAGTTGGTGCTCGCCCTCCTCGAGGTGTTCTCCTGgtgagtttaa ... tatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGG
EST:
gi|71861346|gb|DT010401.1|DT010401EST: CGGACAGGTATGTACGAGTTGGTGCTCGCCCTCCACGAGGTGTTCTCCTG GTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGG
genomic: CGGACAGGTATGTACGAGTTGGTGCTCGCCCTCCTCGAGGTGTTCTCCTGgtgagtttaa ... tatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaagtttttatgtatggctttgatttgtaagtacggctttggctatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT
ctttgat putative branch site (score: 5)
ctatctt putative PPT
tttttatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaccaaagaacagatacaagtggtttccataatttactcttggatgtaagtttttatgtatggctttgatttgtaagtacggctttggctatcttacagGTGGGTCTTCCTGGGACAGGTAAGACTCTCCTAGCAAAGGCTGTGGCTGGGGAGGCTGAAGTGCCTTTTATAAGTTGTTCTGCAAGTGAGTTTGTAGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
-taccaaa
- - - - - - -gatacaa
- - - - - - - - - - - - - - - - - - -ctcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatggct