Sequence
atgc intronic sequence ATGC exonic sequenceGCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATCAAGACCATAACTACATTGTATCCACAAGACATTACCGCGCACCAGAAGTTATCCTAGgtaaacgtttatgactctgacacatctacgtagatgattatttttttgtgtagtcatggtatttaagagtttggaacgtttattgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53570.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53570.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os01g62080.2 (Oryza sativa), 5'ss of exon 10
GCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATCAAGACCATAACTACATTGTATCCACAAGACATTACCGCGCACCAGAAGTTATCCTAGgta--aacgtttatgactctgaca-----catctacgtagatgattatttttttgtgtagtcatg----gtatttaagagtttggaacgtttattgcag--------------------
|| |||||||| |||||||| |||||||||||||| ||||| |||||||| || || | ||||| ||||| ||||| || || || ||||||||||| |||| ||| | || | || | ||| || || | | || | | || || | | | || | ||||| |
GCTATCAAGCTGATTGATTTTGGAAGTACAACATTCGAACACCAAGACCACAATTATGTGGTATCAACAAGGCATTATCGTGCCCCTGAAGTTATCCTTGgtattaacatcatatccttttccatttcccccctataaagtggaacacataattatattactgtgttttgtttatggtacctttgtttagttatttcctttctctgttttcatttgcag
upper sequence: AT3G53570.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 8
GCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATCAAGACCATAACTACATTGTATCCACAAGACATTACCGCGCACCAGAAGTTATCCTAGgtaaacgtttatgact-ctgacacatctac---gtagatgatt-atttttttgtgtagtcatggtatttaagagtttggaacgtttattgcag------------------------------------------
|| |||||||| |||||||| || |||||||| || || |||||||| || || | || || ||||||||||| || ||||||||||||||||| |||| | || | | ||||| || || || | ||| | ||| | | | | | || | || | ||| ||
GCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCCAAGACCACAATTATGTGGTGTCGACAAGACATTATCGTGCACCAGAAGTTATCCTTGgtata-attgacatccgctgacccacacacaaagtggccaatttacctttattttctatttttttcttaatgacaccagtttctttgttttgtatttgttttttaaatctttgataaatgacaattcttgtttag
upper sequence: AT3G53570.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA03G33100.1 (Glycine max), 5'ss of exon 8
GCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATCAAGACCATAACTACATTGTATCCACAAGACATTACCGCGCACCAGAAGTTATCCTAGgtaaacgtttatgactctgacacatctacgtagatgattatt-tttttgtgt---agtcatggtatttaagagtttggaacgtttattgcag
||||| ||||||||||||||||| |||||| ||||||||||||| || || | || |||| || |||||||| || || ||||||||||||||| ||||||| || | | ||| | | | | | || | || | ||| |||||| ||||| ||||| ||| || ||
GCCATTAAGCTCATTGATTTCGGGAGTACATCATTTGAACATCAGGATCACAGTTATGTTGTTTCAACAAGACACTATCGTGCACCAGAAGTTATCTTAGgtaattgtcatt--ccttgaaatgtatgctcaattgctctttatacccatgttccagtcattatatttttc-gtttgttgt-tttcctgtag
upper sequence: AT3G53570.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv08s0040g02640.t01 (Vitis vinifera), 5'ss of exon 8
GCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATCAAGACCATAACTACATTGTATCCACAAGACATTACCGCGCACCAGAAGTTATCCTAGgtaaacgtttatgactctgacacatctacgtagatgattatttttttgt--gtagtcatggtatttaagagtttggaacgtttattgcag
||||| |||||||||||||| || ||||||||||||||||| || || || ||||| | || || |||||||||||||| |||||||| ||||| | ||||| ||| | | | | || |||| || | ||||| | | |||| | | | || | ||| ||||| |||||
GCCATTAAGCTCATTGATTTTGGGAGTACAACATTTGAACACCAGGATCACAACTATGTGGTGTCAACAAGACATTACCGTGCACCAGAGGTTATTTTGGgtaattgttaactcccc--attagactcggtagttggt-attttgatattaatagtttagatgatgaata--ttgttctgtttactgcagMapped 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|163993418|gb|ES077566.1|ES077566EST: TTGTATCCACAAGACATTACCGCGCACCAGAAGTTATCCTAG GGGTTGGATGGAACTATCCATGTGATCTGTGGAGTATTGGTTGCATACTTG
genomic: TTGTATCCACAAGACATTACCGCGCACCAGAAGTTATCCTAGgtaaacgttt ... tttattgcagGGGTTGGATGGAACTATCCATGTGATCTGTGGAGTATTGGTTGCATACTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATCAAGACCATAACTACATTGTATCCACAAGACATTACCGCGCACCAGAAGTTATCCTAGgtaaacgtttatgactctgacacatctacgtagatgattatttttttgtgtagtcatggtatttaagagtttggaacgtttattgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT