Sequence
atgc intronic sequence ATGC exonic sequencegtacgcaaaatgcttctgagtgatgaagtctaagcaccaaaagagttctttttttctttctttccagagtttggtcgcattttttaatttttgataccaatcaatttgatagATGTTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGCTTCCAAAGAATGTCTCTGAAACTGAAGTCCAGTCCTTATTCTCTGAATA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03457.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 3
gtacgcaaaatgcttctgagtgatgaagtctaagcaccaaaagagttctttttttctttctttccagagtttggtcgcattttttaatttttgataccaatcaatttgatagATGTTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGCTTCCAAAGAATGTCTCTGAAACTGAAGTCCAGTCCTTATTCTCTGAATA---------------------------
| ||| | ||||| || | ||||| | || ||| | | | | || |||| ||||| | ||| || | | | ||||| | | ||| ||||||||||||||||||| | || ||||||||||| ||||| | || ||||| | ||||| || ||||
-----------------gtatgaggctctctaa------aattatttcttccataattcatttgtatatcctcagaataattgttaaattttg---ctaatgtatctatgttttcatgttgac-gctgttgct-tccagAGCACAAACTTTTCATTGGAATGCTTCCAAAAAATGTAACAGATGCTGAAATGACTGATTTATTTTCGCAATATGGGAACATCAAGGATTTGCAAATTTT
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G39300.1 (Glycine max), 3'ss of exon 3
gtacgcaaaatgcttctgagt-gatgaagtctaagcaccaaaagagttctttttttctttctttccagagtttggtcgcattttttaatttttgataccaatcaatttgatagATGTTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGCTTCCAAAGAATGTCTCTGAAACTGAAGTCCAGTCCTTATTCTCTGAATA---------------------------
||| || | || | | | ||||| | | || || | ||| || | ||||| || | | | | | ||| || | |||||| | | || || || | |||||||| |||||||| ||| | || ||||||||||||||||| |||||| |||| | | | ||||| | ||
gtataaaatgtttttattatttaatgaaaaattattttcagctga-taaatttcttagcatatgccagaattgctttgtgctatat------tgaggtcatgc--cttgataagtagttttctgtggtccttgaatccagAACACAAACTCTTCATTGGCATGCTTCCAAAGAATGTTTCTGAAGTTGAAATATCTGCTCTTTTCTCCAAGTATGGAACTATAAAGGATTTACAAATTTT
upper sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------gtacgcaaaatgcttctgagtgatgaa-gtctaagcaccaaaaga-gttctttttttctttct--ttccagagtttggtcgcattttttaatttttgataccaatcaatttgatagATG-TTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGCTTCCAAAGAATGTCTCTGAAACTGAAGTCCAGTCCTTATTCTCTGAATA---------------------------
| | ||| | | | || | || ||| ||| |||||| | | | || || | | | | | || || | | | | || ||| || | || | | | ||| ||||||||||||||||||| || ||||||||||| |||||||| |||||| ||||||| || ||||| ||| ||||
gtgtaatatattttcattgtttaattacatatttcatccttaatcttgttcctttttggatgtagcagcgccagttcttattctttatctaatgctgcttttgtaaatgatgtccttgtgctatattatagttttatatatttcaataaataactttttgccatccttgctatccagAGCACAAACTTTTTGTTGGTATGCTTCCGAAGAATGTTTCTGAAGCTGAAGTTTCTTCTTTATTTTCTAAATATGGAACTATAAAAGACTTACAAATTCTMapped 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|47830195|gb|CK119879.1|CK119879EST: ATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG ATGTTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGC
genomic: ATCTAGTCCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAGgtacgcaaaa ... aatttgatagATGTTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGC
EST:
gi|125203382|gb|EL218336.1|EL218336EST: CCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAG ATGTTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGC
genomic: CCGTTGCAAGTTAAGTATGCAGATGGCGAGTTGGAAAGACTAGgtacgcaaaa ... aatttgatagATGTTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttccagagtttggtcgcattttttaatttttgataccaatcaatttgatagATGTTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGCTTCCAAAGAATGTCTCTGAAACTGAAGTCCAGTCCTTATTCTCTGAATA
attttttaatttttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcaaaatgcttctgagtgatgaagtctaagcaccaaaagagttctttttttctttctttccagagtttggtcgcattttttaatttttgataccaatcaatttgatagATGTTCTTGACTGTTCGTGCAATCCAGAGCACAAACTTTTCGTCGGTATGCTTCCAAAGAATGTCTCTGAAACTGAAGTCCAGTCCTTATTCTCTGAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG