Sequence
atgc intronic sequence ATGC exonic sequence...cgtaaccatacatatttttgtgacctcacagttagtatgtagtatagcgtaaattactgggaaagcttgagattcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06400.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 4
cgtaaccatacatatttttgtgacctcacagttagtatgtagtatagcgtaaattactgggaaagcttga--gattcatctatttttctt--ctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
| | ||| ||| | || || | | | || || || | | ||| | |||| || || | | | |||||| || |||| |||||||||||||||||| ||||||| | || |||||||| || | |||||||||||||| |||||||| | |||||||| |||
----ttctttgtgattaaaatgagtccgtcacagactcgtgcaatctcatcagtttatgttaactactaaatgatcattatattcttgttggtttacttgacagGCATAAAAGGAAAGATGAGAGATTACCAACTAGCTGGACTTAATTGGCTCATACGCTTGTATGAGAATGGCATCAATGGAATATTGGCTGATGAGATG
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 4
----cgtaaccatacatatttttgtg-acctcacagttagtatgtagtatagcgtaaattactgggaaagcttgagattcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
|| | | ||||| | || | | | |||| | ||| | | | | ||||| | | | || || | || |||||||| |||||||||||||| ||||||||| | ||||| | ||||||||||| || | |||||||||||||||||||| ||||| || |||||||||
tttttttactttggggtttatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtca--cttgaatgtgacatggcttgtttgt---tcaacagGTATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 4
-cgtaaccatacatatttttgtgacctcacagttagtatgtagtatagcgtaaattactgggaaagcttgag-attcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
|| | ||| || | | || || ||| || | | | | | || | | ||| |||| | || || | |||||||| |||||||| ||||| ||||||||| | ||||| | ||||||||||| || | ||||||||||| |||||||||||||| ||||||||||||
gtgttgtccaacaaatatgtcaatccattcatttataatat--ttttgaattttttgttcacgtgtcatgaatgctcattgttagttttttattctttacagGTATCCAAGGGAAAATGAGGGATTACCAACTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 4
---cgtaaccatacatatt-tttgtg-acctcacagttagtatgtagtatagcgtaaattactgggaaagcttgagattcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
| || | ||| ||||| | || | | | |||| | ||| | | | | ||||| || | | | | || || ||||| || |||||||||||||| ||||||||| | ||||| | ||||||||||| || | |||||||||||||||||||| ||||| || |||||||||
tttttttactttggggattatttgtctaacttgtggattctttgtattcgtatctaatgtttttgtca--cttgaatttgacat---tgcttgttcgttcaacagGCATCCAAGGGAAGATGAGGGATTACCAACTTGCTGGGCTAAACTGGCTCATACGATTGTATGAGAATGGCATAAATGGTATTCTGGCAGATGAAATG
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 4
--cgtaaccatacatatttttgtgacctcacagttagtatgtagtatagcgtaaattactgggaaagcttgagattcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
| | ||| || || || || || || ||| | | | | || | | | |||| || || || |||||||| |||||||| ||||| |||||||| | ||||| | ||||||||||| || | ||||||||||| |||||||||||||| ||||||||||||
tgtattgtctaacaaatacgtg-gatctattcatttata-gtatttttgatttttttttcttgtgtcttgaatgctcattgcttgttttttattcattacagGTATCCAAGGGAAAATGAGGGATTACCAGCTGGCTGGACTAAACTGGCTCATACGATTGTATGAGAATGGAATAAATGGAATTCTGGCTGATGAAATG
upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 4
cgtaaccatacatatttttgtga--cctcacagttagtatgtagtatagcgtaaattactgggaaagcttgagattcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
| | | | | ||| || | | |||||| | | | | | || || | | | | ||| | || |||||||||| || |||||||||||||||||| | ||||| | ||||||||||| || || |||||||||||||| |||||||| || || |||||||||
ttagatcttgctgttgtttaagatgcattacagtt--tttaaaaggtggttattgttgttgtgccctcccccccccccccccccgcccttttttttcctcagGTATTCAGGGAAAGATGAGAGATTACCAACTTGCTGGCCTAAACTGGCTCATACGGCTGTATGAGAATGGCATCAATGGAATCCTCGCAGATGAAATGMapped 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|116436610|gb|EG479202.1|EG479202EST: GGATGGCTTAACTGGATCTGGAAACACACGGTTACTCACACAGCCCTCTT GTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCA
genomic: GGATGGCTTAACTGGATCTGGAAACACACGGTTACTCACACAGCCCTCTTgtaagtacct ... caatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcgtaaattactgggaaagcttgagattcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
ttcatctatttttctt CT-rich tract
attcatctattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgtaaccatacatatttttgtgacctcacagttagtatgtagtatagcgtaaattactgggaaagcttgagattcatctatttttcttctcaatcgacagGTATTCAAGGGAAGATGAGAGATTACCAATTAGCTGGTTTGAACTGGCTCATTCGTCTTTATGAGAATGGCATAAATGGAATTCTTGCTGATGAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT