Sequence
atgc intronic sequence ATGC exonic sequenceTGGTCATGGCTCTAATGTTCAAGGCCTTGAGACAACCGCTACTTTTGATCCAAAGACAGATCAGTTTATCATTCACAGTCCAACTCAGACATCATCCAAAgtaaggggaagaagtatagacagttatctattttgatctctgagtgtttaaattgtgtcttgattttgttttgtttgaaacattag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35690.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM5G864319_T01 (Zea mays), 5'ss of exon 4
TGGTCATGGCTCTAATGTTCAAGGCCTTGAGACAACCGCTACTTTTGATCCAAAGACAGATCAGTTTATCATTCACAGTCCAACTCAGACATCATCCAAAgtaagggg--aagaagtatagacagttatctattttgatctctgagtgtttaaattg--tgtcttgattttgttttgtttgaaacattag------------------------------------------------------
||||||||||| || ||||| |||||||| ||||| || || |||||||||||||| ||| ||||| |||| ||||||||||||| ||| || |||||||| | ||| | || || | || || | | || || | ||| |||||| || || | |||| |
CGGTCATGGCTCAAACGTTCAGGGCCTTGAAACAACTGCCACATTTGATCCAAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTGACCTCCAGCAAAgtaaagtcctgtgaatcaactacctccattttgatttattttaaaaccattcttttcctttccttttttttgtgttactttagccatttgtatcttgttcaaaatcttgtccacaatttgttacatctatcttcatgttggcag
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G052389_T01 (Zea mays), 5'ss of exon 4
TGGTCATGGCTCTAATGTTCAAGGCCTTGAGACAACCGCTACTTTTGATCCAAAGACAGATCAGTTTATCATTCACAGTCCAACTCAGACATCATCCAAAgtaaggggaagaagtatagacagttatctattttgatctct---gagtgtttaaattgtgtcttgatttt-----gttttgtttgaaacattag----------------------------------------------------------------
|||||||||||| || ||||| |||||||| ||||| ||||| || ||||| ||||| ||| ||||| |||| ||||||||||||| || || |||||||| | | || || | | || | ||||| | | | ||| | | | | |||| |||| ||| ||||
TGGTCATGGCTCAAACGTTCAGGGCCTTGAAACAACTGCTACATTCGATCCGAAGACTGATGAGTTTGTCATCCACAGTCCAACTCTCACGTCCAGCAAAgtaaagccctatgg-atcaactgccacct-tattgatttgttaaaaacatttgctcttttccctcttttttcaaaattttctttagcggtttagccatttgtaatgtaaatagttaaagacgctgccccaaaattcattacatgtctcttgttggcag
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ24114 (Selaginella moellendorffii), 5'ss of exon 4
TGGTCATGGCTCTAATGTTCAAGGCCTTGAGACAACCGCTACTTTTGATCCAAAGACAGATCAGTTTATCATTCACAGTCCAACTCAGACATCATCCAAAgtaaggggaagaagtatagacagttatctattttgatctctgagtgtttaaattgtgtcttgattttgttttgtttgaaacattag
||||||||| |||||||| ||||||||||| || || || ||||||||||| ||| || ||||| | || |||| |||| | ||| || | || |||| || | ||| || || | || || || |
TGGTCATGGATCTAATGTCCAAGGCCTTGAAACTACTGCCACTTTTGATCCTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaaa--caaatctttgcgacgagcatt--ttctaataaagctgttttcag-----------------------------------
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ35164 (Selaginella moellendorffii), 5'ss of exon 4
TGGTCATGGCTCTAATGTTCAAGGCCTTGAGACAACCGCTACTTTTGATCCAAAGACAGATCAGTTTATCATTCACAGTCCAACTCAGACATCATCCAAAgtaaggggaagaagtatagacagttatctattttgatctctgagtgtttaaattgtgtcttgattttgttttgtttgaaacattag
||||||||| |||||||| ||||||||||| || || || ||||||||||| ||| || ||||| | || |||| |||| | ||| || | || |||| | || | | || | | ||||| | ||||| |
TGGTCATGGATCTAATGTCCAAGGCCTTGAAACTACTGCCACTTTTGATCCTGCGACCGACGAGTTTGTGATGAACAGCCCAAACCTGACTTCTACAAAGgtaa-----acaaatctttgcaacgagc-attttctaataaagctgttttcag---------------------------------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|116443141|gb|EG485733.1|EG485733EST: CAAAGACAGATCAGTTTATCATTCACAGTCCAACTCAGACATCATCCAAA TGGTGGCCTGGTGGGTTAGGAAAAGTTTTCTACTCACGCTGTTATCTATGC
genomic: CAAAGACAGATCAGTTTATCATTCACAGTCCAACTCAGACATCATCCAAAgtaaggggaa ... gaaacattagTGGTGGCCTGGTGGGTTAGGAAAAGTTT-CTACTCATGCTGTTATTTATGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGTCATGGCTCTAATGTTCAAGGCCTTGAGACAACCGCTACTTTTGATCCAAAGACAGATCAGTTTATCATTCACAGTCCAACTCAGACATCATCCAAAgtaaggggaagaagtatagacagttatctattttgatctctgagtgtttaaattgtgtcttgattttgttttgtttgaaacattag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA