Sequence
atgc intronic sequence ATGC exonic sequencegtaagatgaagatgagattacattgtatcatagctcatttgttaactcatgtaactcttcgttcttatacatgttaaatgtttcagGCATGTTCTTCACAAGTATGCGAACGAAGATGTTTCGCTAGGAGCTTGGTTTATCGGGATTGATGTTAAACACATTGATGATAGAAGATTATGCTGCGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G05170.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 9
---------gtaagatgaagat---gagattacattgtatcat--agctcatttgttaactcatgtaactcttcgttcttatacatgttaaatgtttcagGCATGTTCTTCACAAGTATGCGAACGAAGATGTTTCGCTAGGAGCTTGGTTTATCGGGATTGATGTTAAACACATTGATGATAGAAGATTATGCTGCGGA
|| || | | | |||| || |||| | || | ||| || |||| | | || | | ||||||| ||||||||||||||||||| ||||| ||||| || |||||| | |||||||| || ||||||| | || || |||||| ||||| | || || ||
ctggagtgagtggaattcacctttataaattaaatcaaatcaatgaactaaaaggttcttatattgtgctctcaccctgtgtgtatatgttttctttcagGAATGTTCTTCACAAGTATGCCAACGAGGATGTGTCACTAGGATCCTGGTTTATTGGACTTGATGTGGAGCATATAGATGATCGAAGACTTTGTTGTGGC
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G46230.2 (Glycine max), 3'ss of exon 9
----------gtaagatgaagatg-agattacattgtatca--tagctcatttgttaactcatgtaactcttcgttcttatacatgt-taaatgtttcagGCATGTTCTTCACAAGTATGCGAACGAAGATGTTTCGCTAGGAGCTTGGTTTATCGGGATTGATGTTAAACACATTGATGATAGAAGATTATGCTGCGGA
|||| || | ||| || |||| | || | ||| || |||| | | || | | | ||||||| ||||||||||||||||||| ||||| ||||| || |||||| | |||||||| || ||||||| | || || |||||| ||||| | || || ||
gagtgtgtgtgtaattcacctttgtaagttaaatcaaatcaatgaactaaaaggttcttatattgtgctctcaccctgtgtgtatatgtttttctttcagGAATGTTCTTCACAAGTATGCCAACGAGGATGTGTCACTAGGATCCTGGTTTATTGGACTTGATGTGGAGCATATAGATGATCGAAGACTTTGTTGTGGC
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 9
------------------------------------gtaagatgaagatga--gattacattgtatcatagctcatttgttaactcatgtaactcttcgttcttatacatgttaaatgtttcagGCATGTTCTTCACAAGTATGCGAACGAAGATGTTTCGCTAGGAGCTTGGTTTATCGGGATTGATGTTAAACACATTGATGATAGAAGATTATGCTGCGGA
||| || || | | || || | || | ||| |||| | || | | | | || | || | || ||| ||||||| ||||| ||||||||||| || || ||||| || ||||| |||||||||| || ||||||| || ||||| |||||| ||||| | ||||| ||
gtgagtgcttcatctcacttgtggggaaaaaaacaattaaaatcaaatttatggactaaaatg-gtggtagaaatgttgt-gatccacatgattgcttatttgtgtatttctt---tgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTTGATGTGAATCACATAGATGATCGAAGACTCTGCTGTGGT
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------gtaagatgaagatgag--attacattgtatcatagctcatttgttaactcatgtaactcttcgttcttatac-atgt-taaatgtttcagGCATGTTCTTCACAAGTATGCGAACGAAGATGTTTCGCTAGGAGCTTGGTTTATCGGGATTGATGTTAAACACATTGATGATAGAAGATTATGCTGCGGA
|||| | || || | | | | | | || | | || | | ||| || | |||| | | | | || |||||||||||||||||||||||| || || || ||||| || || |||||||||| || |||||| |||| ||||||||| | |||||||| || ||
gtaagttttcacttaccattttcaaggggtaaaaaaggaatcagcaaattcttggattgatgtatttcataatatcctcttccactttttatggttattttgtacatgattattgcagGCATGTTCTTCACAAGTATGCTAATGAGGACGTTTCACTGGGTTCTTGGTTTATTGGTCTTGATGCGGAACATATTGATGATCGGAGATTATGTTGTGGCMapped 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|164200003|gb|ES121914.1|ES121914EST: CAGTTATACGCCATTTCAAGGGACTTGGCTTCTTATATATCAATCAATCA GCATGTTCTTCACAAGTATGC
genomic: CAGTTATACGCCATTTCAAGGGACTTGGCTTCTTATATATCAATCAATCAgtaagatgaa ... aatgtttcagGCATGTTCTTCACAAGTATGC
EST:
gi|125248703|gb|EL262788.1|EL262788EST: ACTTGGCTTCTTATATATCAATCAATCA GCAAGTTCTTCACAAGTATGCGAACGAAGATGTTTCGCTAGGAGCTTGGTT
genomic: ACTTGGCTTCTTATATATCAATCAATCAgtaagatgaa ... aatgtttcagGCATGTTCTTCACAAGTATGCGAACGAAGATGTTTCGCTAGGAGCTTGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctcatttgttaactcatgtaactcttcgttcttatacatgttaaatgtttcagGCATGTTCTTCACAAGTATGCGAACGAAGATGTTTCGCTAGGAGCTTGGTTTATCGGGATTGATGTTAAACACATTGATGATAGAAGATTATGCTGCGGA
ttatacatgttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatgaagatgagattacattgtatcatagctcatttgttaactcatgtaactcttcgttcttatacatgttaaatgtttcagGCATGTTCTTCACAAGTATGCGAACGAAGATGTTTCGCTAGGAGCTTGGTTTATCGGGATTGATGTTAAACACATTGATGATAGAAGATTATGCTGCGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC