Sequence
atgc intronic sequence ATGC exonic sequence...gattttaggtcttagtaaacagtgtatcttaaataattttcattgtcttcttgtgcacaatccaattaaacttttaatgatgattacaatgttatggcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGGGAGCAATATAGGTTAATGAGAGATGCAATGGAGAAAAGGTTCATCCGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g08630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g16510.1 (Oryza sativa), 3'ss of exon 2
gattttaggtcttagtaaacagt-gtatcttaaataattttcattgtcttcttgtgcacaatccaattaaac--ttttaatgatg--attacaatgttatg----gcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGGGAGCAATATAGGTTAATGAGAGATGCAATGGAGAAAAGGTTCATCCGAG
|| | || |||| | |||| | ||||| | || ||| | ||| ||| ||| || | | | |||| || | | |||||||| || || ||||||||| ||||| | |||||||| |||||||||| ||||| ||||| || ||||||||||||||||||||||| |||||||| |
----ctattttgaggtgaacatttatatcctt-----ttttcctgaactccttacaccaaataaaatgaaatgtcttcagttacaacattattgtgctgtattttacagAGCAAAGACGCTGAAGTGATGTTGAAGATGGGGAGCACCACAGACAAGCGTGAGCAGTATAGATTGATGAGAGATGCAATGGAGAAAAGATTCATCCGGG
upper sequence: Vv17s0000g08630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G806649_T04 (Zea mays), 3'ss of exon 2
gattttaggtcttagtaaacagtgtatcttaaataattttcattgtcttcttgtgcacaatccaattaaacttttaatgatgattaca--atgt----tatggcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGGGAGCAATATAGGTTAATGAGAGATGCAATGGAGAAAAGGTTCATCCGAG
||||| | ||| | | | | | || | || | ||| | | | | ||| || || |||| | | ||||| |||||||| || |||||||||||| | || |||||| | |||||||| || || ||||| || ||||||||||| ||||||||||||||||| || |
----ctaggtgaatagttctaacctattcccagaattgtgaacatgctaccagttgaaaatgccttccg--tgaaagcaatgtttgcaccatgtattgtgtaacagAGTAAGGATGCCGAGGTGATGCTGAAGATGGGAAGCACAACTGACAAGCGTGAACAGTATAGATTGATGAGAGATGCTATGGAGAAAAGGTTCATTCGGG
upper sequence: Vv17s0000g08630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G806649_T02 (Zea mays), 3'ss of exon 2
gattttaggtcttagtaaacagtgtatcttaaataattttcattgtcttcttgtgcacaatccaattaaacttttaatgatgattaca--atgt----tatggcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGGGAGCAATATAGGTTAATGAGAGATGCAATGGAGAAAAGGTTCATCCGAG
||||| | ||| | | | | | || | || | ||| | | | | ||| || || |||| | | ||||| |||||||| || |||||||||||| | || |||||| | |||||||| || || ||||| || ||||||||||| |||||||||||
----ctaggtgaatagttctaacctattcccagaattgtgaacatgctaccagttgaaaatgccttccg--tgaaagcaatgtttgcaccatgtattgtgtaacagAGTAAGGATGCCGAGGTGATGCTGAAGATGGGAAGCACAACTGACAAGCGTGAACAGTATAGATTGATGAGAGATGCTATGGAGAAAAG-----------
upper sequence: Vv17s0000g08630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G09580.1 (Glycine max), 3'ss of exon 2
--gattttaggtcttagtaaacagtgtatcttaaataattttcat-tgtcttcttgtgcacaatccaattaaacttttaatgatgattacaatgttatggcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGGGAGCAATATAGGTTAATGAGAGATGCAATGGAGAAAAGGTTCATCCGAG
| |||| || | || || ||| |||| | | | | | || | ||| | | | |||| || | ||| ||| || ||||||||||||||||||| ||| |||| |||||||||||| ||||||||| ||||||||| | || ||||||||||||||||||||| | ||||| ||||
taggttttttttcatgccaaccatgttattgtaaacattgcttgtctagattatcccaattaattgtggtga--tcttaaggaatttcaca-tgtgttgctagAGCAAGGATGCAGAAGTTATGTTGAAACTTGGGAGCACAGAAGACAAGCGTGAGCAATATCGATTGATGAGAGATGCAATGGAGAAACGATTCATTCGAG
upper sequence: Vv17s0000g08630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G02350.1 (Glycine max), 3'ss of exon 2
--gattttaggtcttagtaaacagtgtatcttaaataattttcat-tgtcttcttgtgcacaatccaattaaacttttaatgatgattaca-atgttatggcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGGGAGCAATATAGGTTAATGAGAGATGCAATGGAGAAAAGGTTCATCCGAG
| || | |||| || || ||| |||| | | | | | || | ||| | | | |||| || | ||| |||||| ||||||||||||||||||| ||| |||| ||||||||||| |||||| || ||||||||| | || ||||||||||||||||||||| | ||||| ||||
taggttctttttcttgccaaccatgttattgtaaacattgcttgtctagattatcccatttaattgtggtga--tcttaaggaatttcacacatgttac--tagAGCAAGGATGCAGAAGTTATGTTGAAACTTGGGAGCACTGAAGACAAACGTGAGCAATATCGATTGATGAGAGATGCAATGGAGAAACGATTCATTCGAG
upper sequence: Vv17s0000g08630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G63000.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------------gattttaggtcttag--taaacagtgtatcttaaataattttcattgtcttcttgtgcacaa--tccaattaaacttttaatgatgattacaatgttatggcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGGGAGCAATATAGGTTAATGAGAGATGCAATGGAGAAAAGGTTCATCCGAG
|| || ||| ||| | ||| | | | | ||| | | || | | ||| | | | | || || | | || |||||||| ||||||||||||||| ||||| | || || |||| || ||||| || ||| | ||||| ||| ||||||||||||||||||||||||||||||
gtatgtctgctttcaatttcagattcaagctcgttacttgtccttgagatttgtgtttcgattccactaccttggtgtaacttagtgacttctggtactagactgaactcataagatatcaaagtttaagacttttagctgaatattatttcctgtgttaaaatcagtg-tgtgtgtggt-ttgaaacagAGCAAAGATGCAGAAGTGATGTTGAAGATGGGTAGTACACAGGATAAGCGTGAACAACACAGGTTGATGCGAGATGCAATGGAGAAAAGGTTCATCCGAGMapped 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|294964888|gb|GW838691.1|GW838691EST: TGCTTGCTGGCATGTTATATGGAGGTAGCAAGGAGGCATCTGCTTCTGTG AGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACATCAGACAAGCGT
genomic: TGCTTGCTGGCATGTTATATGGAGGTAGCAAGGAGGCATCTGCTTCTGTGgtaagttgcc ... gttatggcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcttgtgcacaatccaattaaacttttaatgatgattacaatgttatggcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGGGAGCAATATAGGTTAATGAGAGATGCAATGGAGAAAAGGTTCATCCGAG
ttttaat putative branch site (score: 3)
aattaaacttttaatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattttaggtcttagtaaacagtgtatcttaaataattttcattgtcttcttgtgcacaatccaattaaacttttaatgatgattacaatgttatggcagAGCAAGGATGCAGAAGTGATGCTGAAGCTTGGGAGCACACCAGACAAGCGGGAGCAATATAGGTTAATGAGAGATGCAATGGAGAAAAGGTTCATCCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - aaacagt
- - - - - - - - - - - - - - - aaataat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatcca