Sequence
atgc intronic sequence ATGC exonic sequencegttagaagaaagttacttaaagatctaaacttttatactgttctcttgatctgattcggttttaaatatggtttcgttgttgcagAGATTTCGTGTTGGATGTGGAGTGGAGAGAGACAAACAACGAAGATGAGGATTAAGTATTTAGAAGCAGCTTTGAATCAAGACATTCAGTTCTTTGATAC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G36910.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G36910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G06220.1 (Glycine max), 3'ss of exon 3
-----------gttagaa---gaaagttacttaaagatctaaacttttatact----gttctcttga---tctgattc-----ggttttaaatatggtttc----gttgttgcagAGATTTCGTGTTGGATGTGGAGTGGAGAGAGACAAACAACGAAGATGAGGATTAAGTATTTAGAAGCAGCTTTGAATCAAGACATTCAGTTCTTTGATAC
|| | ||| || || | || | | |||| | | | | | || | ||| | | | | ||| || ||| ||||||||||||||||||||||||||||||| || || | ||| |||||| ||||||||| | |||| | |||||||| ||| | || |||||||| |||||||| ||
gtaaatttcactctaaatttcaaaacttcattctaaatttggaattttgtttttggaaatttttggagggtgtgaatgtggaaagatgttaatctgatttttgttgttgttgcagAGATTTCGTGTTGGATGTGGACAGGTGAACGGCAATCAACGAGGATGAGGATCAGGTATCTGGAAGCAGCGTTGGACCAGGACATTCAATTCTTTGACAC
upper sequence: AT2G36910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G34080.1 (Glycine max), 3'ss of exon 2
--------------------------------------------gttagaagaaagttacttaaagatctaaacttttatactgttctcttgatctgattcg-gttttaaatatggtt-tcgttgttgcagAGATTTCGTGTTGGATGTGGAGTGGAGAGAGACAAACAACGAAGATGAGGATTAAGTATTTAGAAGCAGCTTTGAATCAAGACATTCAGTTCTTTGATAC
| | || || | | ||| | | | | |||| | || ||| | | | | ||| | || ||||||||||||||||||||||||||||| || ||| | ||| | || | |||||| || |||||| |||| || || ||||| || |||||||||||||| || ||
gtcagtgaattgaattgaattgagttgcaattcaattcaattgtctcactgcttctttgtttgtgtttgtctggctttgaattttgattatgatgggtttgaagttgttactgttgttgttgtggttgcagAGATTTCGTGTTGGATGTGGAGCGGGGAGCGGCAATCGACCACGATGAGAATCAAGTATCTAGAGGCTGCGTTGAACCAGGACATTCAGTTCTTCGACAC
upper sequence: AT2G36910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G36820.1 (Glycine max), 3'ss of exon 2
gttagaaga---aagttacttaaagatctaaacttttatac-tgttctcttgatct--gattcggttt--taaatatgg---tttcgttgttgcagAGATTTCGTGTTGGATGTGGAGTGGAGAGAGACAAACAACGAAGATGAGGATTAAGTATTTAGAAGCAGCTTTGAATCAAGACATTCAGTTCTTTGATAC
||||| | || | | || | |||| ||| | |||| ||| | |||| | || | | ||| | | |||||||||||||||||||||||||||||||| || ||| | ||| | || |||||||| || |||||| | || || || || || || |||||||||||||| || ||
gttagtgaattgaattgaattgactcactaattctttgtttgtgtttgtttggctttggattttgattgatgggtttggagttgttgttgttgcagAGATTTCGTGTTGGATGTGGAGCGGGGAGCGGCAATCGACCAAGATGAGAATCAAGTATCTGGAGGCTGCCTTAAACCAGGACATTCAGTTCTTCGACAC
upper sequence: AT2G36910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G20530.1 (Glycine max), 3'ss of exon 2
-----------------------------gttagaagaaagttacttaaagatcta-aacttttatactgttctcttgatctgattcggttttaaatatggtttcgttgttgcagAGATTTCGTGTTGGATGTGGAGTGGAGAGAGACAAACAACGAAGATGAGGATTAAGTATTTAGAAGCAGCTTTGAATCAAGACATTCAGTTCTTTGATAC
|| || | | || | || ||||| | || | | || || | |||| | |||||||||||||||||||||||| |||||||||| || || | ||| |||||| ||||||||| | |||| | || ||||| ||| | || |||||||| |||||||| ||
gtgagtttcactctaaatttcaaaaatttattctaaatttggaattttgtttcttggaatttttagagggtggtgtgaatgtggaaagaagttaatctggttttcgttgttgcagAGATTTCGTGCTGGATGTGGACAGGTGAACGGCAATCAACGAGGATGAGGATCAGGTATCTTGAGGCAGCGTTGGACCAGGACATTCAATTCTTTGACAC
upper sequence: AT2G36910.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g05060.t01 (Vitis vinifera), 3'ss of exon 2
gttagaagaaagttacttaaag-atctaaacttttatactgttctcttgatct--gattcggttttaaatatggtt----tcgttgttgcagAGATTTCGTGTTGGATGTGGAGTGGAGAGAGACAAACAACGAAGATGAGGATTAAGTATTTAGAAGCAGCTTTGAATCAAGACATTCAGTTCTTTGATAC
|| || |||| | | | || | || || |||||| || ||| | || |||| || | || || ||||| || ||||||| |||||||||||||||| |||||||| ||| | || ||||||||||| ||||| ||||||| |||||||| || ||||||||||| ||||| ||
gtgagttgaaattctttctctgtatttgttctgttctactgtgactatggtcttggttttggttgtatagttgcttgaattcgtt-tttcagAGATATCGTGTTGGATGTGGACCGGAGAGAGGCAATCCACCAAGATGAGGATCAAGTACCTAGAAGCGGCTTTGAACCAGGACATTCAGTTTTTTGACACMapped 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|116456352|gb|EG498944.1|EG498944EST: GCTTTACTTTTTAGTGGTTGGTGCTGCAATCTGGGCTTCCTCTTGGGCAG AGATTTCGTGTTGGATGTGGAGTGGAGAGAGACAAACAACGAAGATGAGGA
genomic: GCTTTACTTTTTAGTGGTTGGTGCTGCAATCTGGGCTTCCTCTTGGGCAGgttagaagaa ... gttgttgcagAGATTTCGTGTTGGATGTGGAGTGGAGAGAGACAAACAACGAAGATGAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatactgttctcttgatctgattcggttttaaatatggtttcgttgttgcagAGATTTCGTGTTGGATGTGGAGTGGAGAGAGACAAACAACGAAGATGAGGATTAAGTATTTAGAAGCAGCTTTGAATCAAGACATTCAGTTCTTTGATAC
atctgat putative branch site (score: 4)
tttcgtt putative PPT
ttttaaatatggttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaagaaagttacttaaagatctaaacttttatactgttctcttgatctgattcggttttaaatatggtttcgttgttgcagAGATTTCGTGTTGGATGTGGAGTGGAGAGAGACAAACAACGAAGATGAGGATTAAGTATTTAGAAGCAGCTTTGAATCAAGACATTCAGTTCTTTGATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT