Sequence
atgc intronic sequence ATGC exonic sequenceGCTGTCATTCTATCATCATGGACAGAAAACTATGGAGATCCATCAGAAAACAAGGACTTGCTTACCCAGTTCAGAGGTGCTGCAGTGGCCATTGCCTCTGgtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G27720.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G27720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA04G41090.1 (Glycine max), 5'ss of exon 4
GCTGTCATTCTATCATCATGGACAGAAAACTATGGAGATCCATCAGAAAACAAGGACTTGCTTACCCAGTTCAGAGGTGCTGCAGTGGCCATTGCCTCTGgtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcag
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GCCATCATACTATCTTCATGGACAGAGAATTTTGGGGATCCTTCAGAGAACAAGGACTTGCTTACCCAATTTAGGGGTGCTGCTGTGGCCATTGCTTCTGgtagatt-----tctta-----ccttaaaatttatttttctcattttgatactgtaaatttgaactttgaaactttttatgcatgatgttaatcttttt-aacattttaca-------------------------------
upper sequence: AT4G27720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA06G13760.2 (Glycine max), 5'ss of exon 4
GCTGTCATTCTATCATCATGGACAGAAAACTATGGAGATCCATCAGAAAACAAGGACTTGCTTACCCAGTTCAGAGGTGCTGCAGTGGCCATTGCCTCTGgtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcag
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GCCATCATACTATCTTCATGGTCAGAGAATTTCGGGGATCCTTCAGAGAACAAGGACTTGCTTACCCAATTTAGGGGTGCTGCTGTGGCCATTGCTTCTGgtagat--------ttcttacc---ttaaaatttattttctcattttgatact--gtaaatttgaactttgaaactctttatgtgtgatgttaatctttttaacattttacat-----------------------------
upper sequence: AT4G27720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 5'ss of exon 4
GCTGTCATTCTATCATCATGGACAGAAAACTATGGAGATCCATCAGAAAACAAGGACTTGCTTACCCAGTTCAGAGGTGCTGCAGTGGCCATTGCCTCTGgtgagtaga-aaatcttgttgccccttttagattttacttcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcag
||||||||| | ||||||||| | |||||||| || ||||| ||||| ||||||||||||||||| ||||||| || ||||| || ||||| || |||||| || ||| ||| | | | | || | | | || | |||| || | | | | | | || ||| |
GCTGTCATTTTGTCATCATGGTCTGAAAACTACGGTGATCCTTCAGAGAACAAGGACTTGCTTACACAGTTCAAGGGAGCTGCTGTTGCCATAGCTTCTGgtaggttcccaaagcttttcattgtatgcattgatcctatcttatatgatatcatagcctat---gaatacccatggagtagaccttgaaactctacatacat----------------------------------------
upper sequence: AT4G27720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 5'ss of exon 4
GCTGTCATTCTATCATCATGGACAGAAAACTATGGAGATCCATCAGAAAACAAGGACTTGCTTACCCAGTTCAGAGGTGCTGCAGTGGCCATTGCCTCTGgtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcag
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GCAATCATATTATCATCATGGACTGAAAATTATGGAGATCCTTCAGAAAGCAAGGACTTGCTTATGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTGgtg-------------------------------catttctaactttgctttactttcaactattataaatttatattaattttct-----tcattgctggaaattacgtctagtgaacatggatttggtagctca------Mapped 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|125062675|gb|EL130934.1|EL130934EST: CAAGGACTTGCTTACCCAGTTCAGAGGTGCTGCAGTGGCCATTGCCTCTG ATGAGAAGATAGCACTATTGGGTGCTAT
genomic: CAAGGACTTGCTTACCCAGTTCAGAGGTGCTGCAGTGGCCATTGCCTCTGgtgagtagaa ... cttttatcagATGAGAAGATAGCACTATTGGGTGCTAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCTGTCATTCTATCATCATGGACAGAAAACTATGGAGATCCATCAGAAAACAAGGACTTGCTTACCCAGTTCAGAGGTGCTGCAGTGGCCATTGCCTCTGgtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG