Sequence
atgc intronic sequence ATGC exonic sequencegttttaacaatttcctaaatttgcagatactaaaatttatcctgaataaagttttccgtgactttctggggaaacattctcctcttgcagctactaattcagtacattatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGATGCCACAAACCGAATTAACCTTACACCTGTTGCGTTAATGGAGGCCACCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G24170.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G24170.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA02G08180.1 (Glycine max), 3'ss of exon 10
gttttaacaatttcctaaatttgcagatactaaaatttatcctgaataaagttttccgtgactttctggggaaacattctc-ctcttgcagctactaattcagta---cattatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGATGCCACAAACCGAATTAACCTTACACCTGTTGCGTTAATGGAGGCCACCT
|| | ||||| || ||| | | | | | || | ||| ||| | | | | ||| ||| || | || | | |||| || |||||||| | || | |||||||||||||||||||| || |||| |||||||||||| || ||||| || || || || ||||| || | |
------------------gaatgtaatgtctaaagcaaat--tgatttgaacgattgtttaaaagctagagaatgattatgacgcatagttctaaatgttctgtgatcctttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGATGTCACAAACCGAATGAATCTTACTCCGGTGGCCTTGATGGAAGCATCGT
upper sequence: AT3G24170.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 11
gttttaacaatttcctaaatttgcagatactaaaatttatcctgaataaagttttccgtgactttctggggaaacattctcctcttgcagctactaattcagtacattatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGATGCCACAAACCGAATTAACCTTACACCTGTTGCGTTAATGGAGGCCACCT
| |||| | ||| |||| | | |||| || || | || | | | || | || | | | | | | | || | | |||| || |||||||| || || | |||||||||||||||||||| || |||| |||||||||||| || || || || || || || ||||| || | |
------atgctttcgtcaatgactggatattga-------tttgaacaa--ttgtttaagagctagagaatgattatgactcagttctaaatgttc-tgcgatcctttgtgtttagGTGGATGAGTATTCCCGCACAAGCATACCTAGCATATGGGCTGTGGGTGATGTCACAAACCGAATGAATCTAACTCCGGTGGCCTTGATGGAAGCATCGT
upper sequence: AT3G24170.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 12
gttttaacaatttcctaaatttgcagatactaaaatttatcctgaataaagttttccgtgactttctggggaaacattctcctcttgcagctactaattcagtacattatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGATGCCACAAACCGAATTAACCTTACACCTGTTGCGTTAATGGAGGCCACCT
||| || || | | ||||| | | || || | | |||| | || | | | || | | | | ||||| || ||||| || || ||||| ||||||||||||||||| | || |||| ||||| ||||| || ||||| ||||| || |||||||||| ||||
------------tcccctgttctcatgaaacagaattttttatttat----ttatttatttttttccagcataaaaagttaataaccagactgaagttctcctgttgtttttccagGTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGATGTTACAAATCGAATGAATCTTACCCCTGTGGCCTTAATGGAGGGAACCTMapped 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|116457529|gb|EG500121.1|EG500121EST: TGAATTTAGAAGCTGTTGGTGTTGAACTTGATCAGGCTGGAGCTGTGAAG GTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGAT
genomic: TGAATTTAGAAGCTGTTGGTGTTGAACTTGATCAGGCTGGAGCTGTGAAGgttttaacaa ... ttatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGAT
EST:
gi|152034638|gb|BP833544.2|BP833544EST: TGAATTTAGAAGCTGTGGGTGTTGAACTTGATCAGGCTGGAGCTGTGAAG GTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGAT
genomic: TGAATTTAGAAGCTGTTGGTGTTGAACTTGATCAGGCTGGAGCTGTGAAGgttttaacaa ... ttatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGAT
EST:
gi|125062833|gb|EL131032.1|EL131032EST: CTGGAGCTGTGAAG GTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGAT
genomic: CTGGAGCTGTGAAGgttttaacaa ... ttatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctggggaaacattctcctcttgcagctactaattcagtacattatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGATGCCACAAACCGAATTAACCTTACACCTGTTGCGTTAATGGAGGCCACCT
tactaat putative branch site (score: 1)
ttatcctc putative PPT
tactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttaacaatttcctaaatttgcagatactaaaatttatcctgaataaagttttccgtgactttctggggaaacattctcctcttgcagctactaattcagtacattatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGATGCCACAAACCGAATTAACCTTACACCTGTTGCGTTAATGGAGGCCACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG