Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtggaatctttttcttcttgtttggtttttaagcgactctttgttgtgtgtttgattgttgtgtaattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46860.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 2
-----------------------gtaaagtggaatctttttcttcttgtttggtttttaagcgactctttgttgtgtgtttgattgttgtgtaattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCA
| ||| || | | | ||| ||| | | | || | ||| |||| ||| | || | | || | || || |||||||| ||||| ||||| |||| ||| || ||||| ||| | ||||| |||||||||||||||| || | ||||||||| |
tatgaatctatgatcattactattttaaggaacatttctatgttccatttttgctgatgtattacacaatgt-gtgttgatgacc-tcgtttggaactacagGCCAGCAAAAAGATTGCTGATGCGAAGCTAGCAAAGGATTTCCAAGCAGTTCTGAAAGAATTTCAGAAAGCTCAACGGTTAGCGGTAGAAAGAGAAGCTG
upper sequence: AT5G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 2
-----------------gtaaagtggaatctttttcttcttgtttggtttttaagcgactctttgttgtgtg---tttgat-tgttgtgtaattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCA
| | || | | || | | ||| |||| || ||| || || | ||| | | || || ||||||||||||| |||||||| |||||||||| || ||||| || || || ||||| |||||||| ||||| | | | ||||| || |||||
aatgtttgttgtagtttatgtactgaattattagtggcgtgatttttttttcccttgaggaaagaaaaagtgaccttcaatgtcttggttgtatttgcagACAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAG
upper sequence: AT5G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G01960.1 (Glycine max), 3'ss of exon 2
--------------------gtaaagtggaatctttt-tcttcttgtttggtttttaagcgactctttgttgtgtgtttgattgttgtgtaattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCA
| | ||||| | | |||||| || || | || | | ||| | | || || ||||||||||||| |||||||| |||||||||| || ||||| || || || ||||| |||||||| || || | | | || || || |||||
agctttatgtactgaattattggtggcgcgatcttgaatttatttgtttttcccttgaggaaagaaaaagtgaccttcaatgtattggttgtatttgcagGCAAGTAAGAAGATAGCAGATGCGAAGCTTGCAAAAGATTTTCAGGCGGTGTTGAAAGAATTTCAGAAGGCACAGCGTCTTTCAGCGGAGAGGGAAACTG
upper sequence: AT5G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G08200.1 (Glycine max), 3'ss of exon 2
-----------------gtaaagtggaatctttttctt-cttgtttggtttttaagcgactctttgttgtgtgttt---gattgttgtgtaattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCA
|| | | | ||| | ||| || | | || || || | | || ||| | || | | || || | || || |||| |||||||||||||||||||| ||||| | || ||||| || || || |||||||||||||| || |||| ||| ||||| || |||||
atactgtgaaaacttgtgttacgggcaatgtctttattgcattttagggttccatgaccttccatgtcttttgcctcaaaaacatttcttattattgcagGCAAGCAAGAAGATTGCAGATGCTAAACTTGCGAAAGATTTTCAGGCAGTGTTGAAAGAGTTTCAGAAGGCACAACGTCTTGCAGCTGAGAGGGAAACAG
upper sequence: AT5G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------gtaaagtggaatctttttcttcttgtttggtttttaagcgactctttgttgtgtgtttgattgttgtgtaattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCA
| | | || || | ||| ||||| | | | | || | | ||| || || | || |||||||||||||||||||| || |||| || |||||||| |||||||||||||||||||| ||||||| || || ||||| |||||
tttggatatgttagaaaaaggaaacagaagaggatgcttccagtgctgtgatcttttttgaggggtgtaattgccttgaacattctccatctaactgc--agGCCAGCAAGAAGATTGCAGATGCTAAACTGGCAAAAGATTTTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGGMapped 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|125293005|gb|EL307090.1|EL307090EST: AAACTGATCATCAAAGCGGTGTCAAT CCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTT
genomic: AAACTGATCATCAAAGCGGTGTCAATgtaaagtgga ... aattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTT
EST:
gi|86038438|gb|DR334193.1|DR334193EST: CAGCTAAACTTAAAGAAGCTAGTGAAACTGATCATCAAAGCGGTGTCAAT CCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTT
genomic: CAGCTAAACTTAAAGAAGCTAGTGAAACTGATCATCAAAGCGGTGTCAATgtaaagtgga ... aattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttggtttttaagcgactctttgttgtgtgtttgattgttgtgtaattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCA
gtttgat putative branch site (score: 5)
tttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtggaatctttttcttcttgtttggtttttaagcgactctttgttgtgtgtttgattgttgtgtaattgtgtagCCAAGTAAGAAGATTGCAGATGCTAAGCTTGCAAGGGACTTTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA