Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcaagtcttttccgtattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttagATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAGGAACATGATCCTATTTGGCTAGAGCTTCGACATGCACATATAGCAGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G12360.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 11
-----gtaagttcaagtcttttccgtattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttagATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAGGAACATGATCCTATTTGGCTAGAGCTTCGACATGCACATATAGCAGAT
|| | | || || | | | | |||||| || ||| || |||| | | | | | || | | | || | || || |||| ||||| | || || | ||| ||| ||||| || || || ||||| ||||||||||| ||||| || ||||| ||||||||||| ||||||
gtgttctataatatctttttccccctctaaactgttgtgactt-gtgtccactttcttgttataaatacaa----atatac-tgtattcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTTTTGGAGGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 10
-----gtaagttcaagtcttttccgtattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttagATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAGGAACATGATCCTATTTGGCTAGAGCTTCGACATGCACATATAGCAGAT
|| | || || || | | | || |||||| || ||| | || |||| || | | || | | | || | || || |||| ||||| | || || | ||| ||| ||||| || ||||| || || ||||||||||| ||||| || ||||| ||||||||||| ||||||
gtattctacaatattgttttccccctctaaattgttgtgactt-gtgttcactttcttgtcatgaacacaa----atctac-tgtattcttaagGTTCCTAGCAAGACTGGTGGTCCACCTGAGCGAAAAGAGGTTCTCTTGGACGATCATGATCCTATATGGCTTGAACTTCGTCATGCACATATTGCAGAT
upper sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 10
gtaagttcaagtcttttccg-----tattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttagATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAGGAACATGATCCTATTTGGCTAGAGCTTCGACATGCACATATAGCAGAT
||| ||||||| |||| | || || |||| | | | | | | | ||| | || ||||||| ||||||| ||| |||| || | ||||||||| ||||| || || || ||||| ||||||||| | ||||| ||||| || ||||||||||||||||||
------gtaagccttttccaaattttatttatgcttttggatttgatattgtttttcctttagctgtgtgtgttgaggaattattcctttttagGTTCCAAGTAAAACAGGTGGTCCACCAGAGAAAAAAGAAGTCCTTTTGGAGGATCATGATCCTGTCTGGCTTGAGCTCCGCCATGCACATATAGCAGATMapped 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|164018015|gb|ES008208.1|ES008208EST: GAACATGGAAGGAAACAAATATGTACATGTG ATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAG
genomic: GAACATGGAAGGAAACAAATATGTACATGTGgtaagttcaa ... tagtttttagATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttagATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAGGAACATGATCCTATTTGGCTAGAGCTTCGACATGCACATATAGCAGAT
ttcattt CT-rich tract
ttcatttagttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcaagtcttttccgtattagttattgtgattttgtggtggctctcttcctggatactccatgtgatgttcatttagtttttagATTCCAAGCAAATCAGGCGGACAACCAGAGAAGAAAGATGTGCTCTTAGAGGAACATGATCCTATTTGGCTAGAGCTTCGACATGCACATATAGCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT