Sequence
atgc intronic sequence ATGC exonic sequence...gaattgtattttgaacaaagaaaaatccagacctcctgtgttctactttcagacagtagttttttttgtgtattgagcttaatgtcatgctatgttacagGAAACAAAGGTGCAGGCCGGCCTCCATTGAACTGGGAAGTCAGATCAGGCATCGCCCTTGGAGCTGCTCGTGGCTTAGACTATCTTCACTCACAAGACCC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G17840.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G17840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G33700.1 (Glycine max), 3'ss of exon 1
gaattgtattttgaacaaagaaaaatccagacctcctgtgttctactttcagacagtagttttttttgtgtattgagcttaatgtcatgctatgtt-acagGAAACAAAGGTGCAGGCCGGCCTCCATTGAACTGGGAAGTCAGATCAGGCATCGCCCTTGGAGCTGCTCGTGGCTTAGACTATCTTCACTCACAAGACCC
|| | | | | | | | |||| | | | ||| || || | ||| || ||| | | ||| ||||| |||||||||||||| || || || | ||| |||| |||||||| ||||||||||| || ||||||||||| |||||| | || || || || |||| || ||
-tatggctctccatctcatgctataactagactagggataattgaatttggcactgttgatttccaacagtggtgatgatggatgcttgcgatgtttacagGAAACAAAGGAGCTGGTAGGACACCACTGAATTGGGAAGTGAGATCAGGCATTGCACTTGGAGCTGCCCGTGGCATTGAGTACCTACATTCACGAGGGCC
upper sequence: AT3G17840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G06020.1 (Glycine max), 3'ss of exon 1
gaattgtatt-ttgaacaaagaaaaatc--cagacctcctgtgttctactttcagacagtagttttttttgtgtattgagcttaatgtcatgctatgttacagGAAACAAAGGTGCAGGCCGGCCTCCATTGAACTGGGAAGTCAGATCAGGCATCGCCCTTGGAGCTGCTCGTGGCTTAGACTATCTTCACTCACAAGACCC
| || | | || | | | | ||| | | | | ||||| | | || || | || | || | | |||||||||||||||| || || || | ||| |||| |||||||| ||||||||||| || ||||||||||| |||||| | || || || || |||| || ||
--ctgctactactagactaggcttagttggtagaatttggctatgttgatttcatgagtttctaaacagtggtgatgatgtttctgattctgatct-ttacagGAAACAAAGGAGCTGGTAGGACACCACTGAATTGGGAAGTGAGATCAGGCATTGCACTTGGAGCTGCCCGTGGCATTGAGTACCTACATTCACGAGGGCC
upper sequence: AT3G17840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0000g02010.t01 (Vitis vinifera), 3'ss of exon 1
-----gaattgtattttgaacaaagaaaaatccagacctcctgtgttctactttcagacagtagttttttttgtgtattgagcttaatgtcatgctatgttacagGAAACAAAGGTGCAGGCCGGCCTCCATTGAACTGGGAAGTCAGATCAGGCATCGCCCTTGGAGCTGCTCGTGGCTTAGACTATCTTCACTCACAAGACCC
||||| | || | ||| | || || | | | || | || | ||| || | ||| | | | ||||| |||||||||||| ||||| || |||||||||| |||||| |||||||||| || || ||||||||||||||||| | || || || ||||| |||| ||
actaagaatttggtatt-agcaagttggattctggaaccctagaa----acacttgattagcattttccttattacattaccatctctcttgaatcttgttatagGAAACAAAGGAGCAGGTAGGACTCCATTGAATTGGGAAATCAGATCAGGGATTGCTCTTGGAGCTGCTCGTGGTATTGAATACCTACACTCTCAAGGTCCMapped 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|164043141|gb|ES134297.1|ES134297EST: CTTGTCTATGACTTTCATGCCTATGGGAAGCTTATCAGCTCTCTTACACG GAAACAAAGGTGCAGGCCGGCCTCCATTGAACTGGGAAG
genomic: CTTGTCTATGAC-TTCATGCCTATGGGAAGCTTATCAGCTCTCTTACACGgtgagaacta ... tatgttacagGAAACAAAGGTGCAGGCCGGCCTCCATTGAACTGGGAAG
EST:
gi|164221791|gb|ES058705.1|ES058705EST: GGGAAGCTTATCAGCTCNCTTACACG GAAACAAAGGTGCAGGCCGGCCTCCATTGAACTGGGAAGTCAGATCAGGCA
genomic: GGGAAGCTTATCAGCTCTCTTACACGgtgagaacta ... tatgttacagGAAACAAAGGTGCAGGCCGGCCTCCATTGAACTGGGAAGTCAGATCAGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcagacagtagttttttttgtgtattgagcttaatgtcatgctatgttacagGAAACAAAGGTGCAGGCCGGCCTCCATTGAACTGGGAAGTCAGATCAGGCATCGCCCTTGGAGCTGCTCGTGGCTTAGACTATCTTCACTCACAAGACCC
gcttaat putative branch site (score: 4)
ttttttttgtgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaattgtattttgaacaaagaaaaatccagacctcctgtgttctactttcagacagtagttttttttgtgtattgagcttaatgtcatgctatgttacagGAAACAAAGGTGCAGGCCGGCCTCCATTGAACTGGGAAGTCAGATCAGGCATCGCCCTTGGAGCTGCTCGTGGCTTAGACTATCTTCACTCACAAGACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - -caaagaa
- - - - - - - - - - - - - ccagacc