Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgtgtttttagcttagcaaagtaatgttgttccatctttgaaaaatctgccctgaacatcttttcgtgtgacagCCGAGTGCACTGCTGCTGATGCTTTCAAACACGCCGGAGGAAACATTGTCTTTGCAAGTGGAAGTCCATTTGAGAACGTTGAACTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G00570.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA18G46340.1 (Glycine max), 3'ss of exon 13
----gtttgtgtgtttttagcttagcaa--agtaatgttgttccatctttgaaaaatctgccctgaacatcttttcgt-------gtgacagCCGAGTGCACTGCTGCTGATGCTTTCAAACACGCCGGAGGAAACATTGTCTTTGCAAGTGGAAGTCCATTTGAGAACGTTGAACTTG
|||||| | | |||| | | |||| || | | ||| || ||| || |||||||| |||||||||||| ||| ||||||| || || |||| ||| || || |||||||||||||| || ||||| || || || ||||
gtttgtttgtacacggctcattcagcactcacaattgtttaataatgtccatgtttttcattttgactattgttttgttatcattgtgacagCTGAGTGCACTGCTATTGAAGCTTTCAGTCATGCAGGAGAAAATATAGTGTTTGCAAGTGGAAGCCCTTTTGAAAATGTAGATCTTG
upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv15s0046g03670.t01 (Vitis vinifera), 3'ss of exon 13
-----------------gtttgtgtgtttttagcttagcaaagtaatgttgttccatctttgaaaaatctgccctgaacatcttttcgtgtgacagCCGAGTGCACTGCTGCTGATGCTTTCAAACACGCCGGAGGAAACATTGTCTTTGCAAGTGGAAGTCCATTTGAGAACGTTGAACTTG
| | || | | | | | | | | || | | | | | || ||| || | || ||| |||||||| ||||||||||||||||| || || |||| ||| ||||| ||||||||||| ||||| |||| || ||| | || |
gtttgtgttgcaaaccctatcaagcacttacatttatttcaggcagacatatggcctccattgacatttttttctttgcatattct-atggtgtagCTGAGTGCACAGCTGCTGATGCTTTCAAGCATGCAGGAGAAAATATTGTTTTTGCAAGTGGGAGTCCTTTTGCAAATGTTAATCTAG
upper sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ19450 (Selaginella moellendorffii), 3'ss of exon 13
gtttgtgtgtttttagcttagcaaagtaatgttgttccatctttgaaaaatctgccctgaacatcttttcgtgtgacagCCGAGTGCACTGCTGCTGATGCTTTCAAACACGCCGGAGGAAACATTGTCTTTGCAAGTGGAAGTCCATTTGAGAACGTTGAACTTG
| || | | || ||| | || | ||| | | || | | |||| || ||||| || | || || || || | | |||| ||||| ||||||||||||||||||| ||||| |||| |||||||
--------------------gtaagttgttattactccggc---gacacgcatgctaagtaagctttccattttttcagCTGAATGCACAGCAGAAGAAGCATTTAAGAATGTGGGAGATCACATTATCTTTGCAAGTGGAAGTCCTTTTGATGACGTGGAACTTGMapped 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|125219924|gb|EL234009.1|EL234009EST: TGACTCATGCAAGCCTGCCATTTTTGCCATGTCGAATCCCACTTTGAATG CCGAGTGCACTGCTGCTGATGCTTTCAAACACGCCGGAGG
genomic: TGACTCATGCAAGCCTGCCATTTTTGCCATGTCGAATCCCACTTTGAATGgtttgtgtgt ... cgtgtgacagCCGAGTGCACTGCTGCTGATGCTTTCAAACACGCCGGAGG
EST:
gi|116463393|gb|EG505985.1|EG505985EST: TGACTCATGCAAGCCTGCCATTTTTGCCATGTCGAATCCCACTTTGAATG CCGAGTGCACTGCTGCTGATGCTTTCAAACACGCCGGAGGAAACATTGTCT
genomic: TGACTCATGCAAGCCTGCCATTTTTGCCATGTCGAATCCCACTTTGAATGgtttgtgtgt ... cgtgtgacagCCGAGTGCACTGCTGCTGATGCTTTCAAACACGCCGGAGGAAACATTGTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtaatgttgttccatctttgaaaaatctgccctgaacatcttttcgtgtgacagCCGAGTGCACTGCTGCTGATGCTTTCAAACACGCCGGAGGAAACATTGTCTTTGCAAGTGGAAGTCCATTTGAGAACGTTGAACTTG
catcttttc CT-rich tract
tttgaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgtgtttttagcttagcaaagtaatgttgttccatctttgaaaaatctgccctgaacatcttttcgtgtgacagCCGAGTGCACTGCTGCTGATGCTTTCAAACACGCCGGAGGAAACATTGTCTTTGCAAGTGGAAGTCCATTTGAGAACGTTGAACTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG