Sequence
atgc intronic sequence ATGC exonic sequencegtcattgttgctcttcgaaattgtttctcagatttataagtgtttttgattgatctagtatccaatcgtcttagctagtcttatgtagtttagtttctgtataacagGAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G27450.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G07960.1 (Glycine max), 3'ss of exon 2
gtcattgttgctcttcgaaattgtttctcagatttataagtgtttttgattgatctagtatccaatcgtcttagctag-tcttatgtagtttagtttctgtataa---cagGAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG
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----ttgt-gcagatagtaatt-ttactggacttgttaattctgacagaaaactctgatg---ggttgttttgtttggatcatatttaat--gatttatgactaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG
upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G39210.1 (Glycine max), 3'ss of exon 2
gtcattgttgctcttcgaaattgtttctcagatttataagtgtttttgattgatctagtatccaatcgtcttagctagtcttatgtagtttagtttctgtataacagGAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG
|||||| | | | |||| || || | | | | || | | | | | ||| || | || ||| | | || || |||||||| |||||||| |||||||||||||| ||||| ||||| || ||| || | |||| ||||| | ||| ||||||| || || ||
--cattgtagagata-gtaatt--ttactggactcgttaattcagatggaaaaccctgattgcttgcgtgtttg--gatcatattaatgacatttgactaatttcagGAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAGAGAGAGGAGTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG
upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G31100.1 (Glycine max), 3'ss of exon 2
gtcattgttgctcttcgaaattgtttctcagatttataagtgtttttgattgatctagtatccaatcgtcttagctagtcttatgtagtttagtttctgta-taacagGAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG
|||||| | | | |||| || || | | | | || | | | | ||| || | || ||| || | |||| || | ||||| || |||||||| |||||||||||||| |||||||||| || |||||| | |||| ||||| | ||| ||||||| || || ||
--cattgtagagata-gtaatt--ttactggactcgttaattcagatggaaaaccctgattggttgcgtgtttg--gatcatat-taatgatgtttgaataatttcagGAGCTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGTGGATTTCTTTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG
upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G31100.2 (Glycine max), 3'ss of exon 3
----gtcattgttgctcttcgaaattgttt--ctcagatttataagtgtttttgattgatctagtatcca-atcgtcttagctagtcttatgtagtttagtttctgtataacagGAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG
| || || | | | | | || |||||| | || |||||| | || | ||| | ||| | || || ||| ||||| || |||||||| |||||||||||||| |||||||||| || |||||| | |||| ||||| | ||| ||||||| || || ||
tgtagagatagtaattttactggactcgttaattcagatggaaaa----ccctgattggttgcgtgtttggatcatattaatgatgtttgaataattt-------------caggagCTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGTGGATTTCTTTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG
upper sequence: AT2G27450.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0080g00560.t01 (Vitis vinifera), 3'ss of exon 2
gtcattgttgctcttcgaaattgtttctcagatttataagtgtttttgattgatctagtatccaatcgtcttagctagtcttatgtagtttagtttctgtataacagGAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG
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-caataaatgctttt-aacaccataccacaaaggagtagctctccctaaatccttta-tattcatttttagttttta-ccttgtgtgcttatgggttcatc---cagGAACTATTTGAAGGATATTACTTCTGTCAAGCACAGAGGGAGGATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGMapped 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|125204311|gb|EL219265.1|EL219265EST: AGAAGCTCACGCTAAAGGAGCTAATATCATTCTTATTCAG GAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTT
genomic: AGAAGCTCACGCTAAAGGAGCTAATATCATTCTTATTCAGgtcattgttg ... tgtataacagGAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctagtatccaatcgtcttagctagtcttatgtagtttagtttctgtataacagGAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG
gattgat putative branch site (score: 4)
tttctgt putative PPT
tttagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcattgttgctcttcgaaattgtttctcagatttataagtgtttttgattgatctagtatccaatcgtcttagctagtcttatgtagtttagtttctgtataacagGAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC