Sequence
atgc intronic sequence ATGC exonic sequencegtaaatttttgttccttttcttctttattttagcagattctgttttgttggatactgcttttaattcaaaatgtagtcatggttcaccaattctatgcttatctattttgtgtgttgtcagGTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGCTGCTCTTTACTTTTGGCAGATACCTCATTTTATGGCCCTTGCACATCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G44520.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G44520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g34390.1 (Oryza sativa), 3'ss of exon 4
gtaaatttttgttccttttcttctttattttagcagattctgttttgttggatactgcttttaattcaaaatgtagtcatggtt-caccaattctatgcttatctattttgtgtgttgt-cagGTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGCTGCTCTTTACTTTTGGCAGATACCTCATTTTATGGCCCTTGCACATCTC
|| ||| | | | || | | |||| || | | | | | ||| | || | || | |||| | | | | ||| ||||||||| ||||| || | | | ||| ||| | |||||||| || ||||| | |||| |||||| ||||| |||||||||||||||||| | |
--------------------atcagtatgtgtcaatgtcctatct-gttgaatgccaatgagggaccttttttt--ccattgccacatgatctcagtccttaatttcatcttcttctgtacagGTGGGCAGCAGCTTCGTCTGAACTGTCACTGAATGCTATGATTCTCCCTGCTGCATTGTACTATTGGCAAATACCACATTTTATGGCCCTTGCATACTTA
upper sequence: AT2G44520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 4
gtaaatttttgttccttttcttctttattttagcagattctgttttgttggatactgcttttaattcaaaatgtagtcatggttcaccaattctatgcttatctattttgtg-tgttgtcagGTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGCTGCTCTTTACTTTTGGCAGATACCTCATTTTATGGCCCTTGCACATCTC
| |||| | |||| || | || | |||| ||| | | | | | ||| |||| || | | || | | |||| ||| | | | ||||||||| ||||| || | | | ||| || ||||||| || || || || | ||||||||||| ||||||||||||||||| || || | |
---------agagtatttttgttcttatccta------tttgatacgttgaata-----tgtcagtagagttgtgtacatgttttgtaagat--gtgatcctttattgtgtcctctggacagGTGGGCAGCAGCTTCAACTGAACTGTCACTAAACGCGATGATACTCCCTGCCGCATTGTACTTTTGGCAAATACCTCATTTTATGGCTCTCGCGTACTTA
upper sequence: AT2G44520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G38710.1 (Glycine max), 3'ss of exon 4
gtaaatttttgttccttttcttctttattttagcagattctgttttgttggatactgcttttaattcaaaatgtagtcatg-gttcaccaattctatgcttatctattttgtgtgttgtcagGTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGCTGCTCTTTACTTTTGGCAGATACCTCATTTTATGGCCCTTGCACATCTC
|| ||| |||||| | || | | ||| | | | ||||| |||| | || || | || || | | | |||| || |||| ||||| ||||| ||| | | |||||| ||| |||||||||||||||||| | || |||||||| ||||| |||||||||||||| || || |
----------tctctcttttttctttttctttactcacgttgtctcact------------tcattcaccatgtgtacgtgtattttctgcccctcatctcctttttgttgttgattttcagATGGGCTGCAGCTTCTAATGATATTTCACTAAATGGAATGATTCTTCCAGCTGCTTTGTATTTTTGGCAAATACCACATTTTATGGCCCTAGCCTATTTG
upper sequence: AT2G44520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0021g00430.t01 (Vitis vinifera), 3'ss of exon 4
gtaaatttttgttccttttcttctttattttagcagattctgttttgttggatactgcttttaattcaaaatgtagtcatggttcaccaattctatgcttatctattttgtgtgttgtcagGTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGCTGCTCTTTACTTTTGGCAGATACCTCATTTTATGGCCCTTGCACATCTC
| || | || | || | | || ||| | | | | || || | || |||| ||||| ||||| || || |||||||| ||||| | || ||| ||||| |||| ||||||||||| ||||| || || |||||||| ||||| |||||||||||||| ||| | |
---------------gtatcaaatgcatgcatgtgcatacaaacattctgcatatcatatccact---ggctatatatctgatctgacatgctcatgcctatctgttttgggtttt---agGTGGGCTGCAGCTGCCGGACAGGTTTCACTCAATGGAATGATTCTTCCTGCTGCCCTCTATTTTTGGCAAATACCCCATTTTATGGCCCTAGCATACTTGMapped 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|116390645|gb|EG433237.1|EG433237EST: ATCAATACATGGGTTGGCGCTGTTGTTGGTGCTATCCCACCCTTGCTTGG GTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGC
genomic: ATCAATACATGGGTTGGCGCTGTTGTTGGTGCTATCCCACCCTTGCTTGGgtaaattttt ... gtgttgtcagGTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaaatgtagtcatggttcaccaattctatgcttatctattttgtgtgttgtcagGTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGCTGCTCTTTACTTTTGGCAGATACCTCATTTTATGGCCCTTGCACATCTC
ttatctatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatttttgttccttttcttctttattttagcagattctgttttgttggatactgcttttaattcaaaatgtagtcatggttcaccaattctatgcttatctattttgtgtgttgtcagGTGGGCGGCAGCGTCTGGTCAGATTTCATACAATTCGATGATTCTTCCAGCTGCTCTTTACTTTTGGCAGATACCTCATTTTATGGCCCTTGCACATCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT