Sequence
atgc intronic sequence ATGC exonic sequencegttttatatctttaacttactgtcagcttcttcatatcatgtatatgttgtttctcatttttgcttcgatatttccagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGCAAACAATCAAATTATAAACTATAAGTGCTCTCCTAATGAGAAGTGGTTGGTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11130.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 4
------------------------------gttttatatctttaacttactgtcagcttcttcatatcatgtatatgttgtttctcatttttgcttcgatatttc------cagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGCAAACAATCAAATTATAAACTATAAGTGCTCTCCTAATGAGAAGTGGTTGGTCTT
|| ||| ||| | | | ||||||| || | | | ||||||| | || | | |||| |||||||| || | |||||||| ||||| |||||||||||||| |||||||||||||| |||||| || ||| |||||||||| | || |
gtattgaactattgatctgaacttttgtccaattattattcgctgctttgcattatttggatcatatc-catacaaaccaatgattttttttgcatgtatttgttgtaatacagGAGATTCTGAACCGGCCAAGATGTTCGATAGGACGGCTAATTTGGCCAACAATCAAATTATCAACTATCGATGTGATCCATCTGAGAAGTGGCTTGTGCT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------gttttatatctttaacttactgtcagcttcttcatatcatgtatatgttgtttctcatttttgc-ttcgatatt-tccagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGCAAACAATCAAATTATAAACTATAAGTGCTCTCCTAATGAGAAGTGGTTGGTCTT
| | ||||| || | || || || | ||||||| |||||| | | || || | | | | |||| |||||||| || | |||||||| ||||| |||||||||||||| |||||||||||||| |||||| || ||| |||||||||| | || |
gtattgaactattgatctgaacttttgtccaattattattcgctgctttgcattatttggatcatatccata-caaaccaatgatttttt--ttgcatgtatttgttgtaatttttgcatgtatttgttgtaatacagGAGATTCTGAACCGGCCAAGATGTTCGATAGGACGGCTAATTTGGCCAACAATCAAATTATCAACTATCGATGTGATCCATCTGAGAAGTGGCTTGTGCT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 4
---------------------------------------gttttatatctttaacttactgtca-gcttcttcatatcatgtatatgttgtttctcatttttg-cttcgatat-------ttccagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGCAAACAATCAAATTATAAACTATAAGTGCTCTCCTAATGAGAAGTGGTTGGTCTT
||||| | | || | | | || || | | | || | | || |||| || ||||| || |||||| ||||| || || ||||||||||| ||||| || |||||||||||||||||||| || || |||| || |||| |||||| |||||||||||
gtaagacaatgataaacttcaattctgcttaactacatggttttgtgccgttttccagtttttgcactgctgttcagtgttattttgctaatcggtatatttgtctgtgatatatgtaacttgtagGTGACTCTGAACCTGTAAAGATGTTTGAGAGAACAGCAAATTTGGCAAACAATCAAATAATTAATTATAGATGTGATCCTTCTGAGAAATGGTTGGTCTT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------gttttatatctttaacttactgtcagcttcttcatatcatgtatatgt-tgtttctcatttttgcttcgatatttccagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGCAAACAATCAAATTATAAACTATAAGTGCTCTCCTAATGAGAAGTGGTTGGTCTT
|| || | | | | | || | |||| || || | | || | |||| | || | || |||||| ||||| || |||||||||||||| ||||| || |||||||||||||| || || || || ||| || |||| || || |||||||| ||
gtaagatgataatttgcttaactaaatatttttgtgttatactatattttccagtttacgtattctttatgcagtgtgcttgtggtttctgcaaattgttgactggtacatggttcatgat--ctatataacttgtagGTGACTCTGAACCTGTTAAGATGTTTGAGAGAACAGCAAATTTGGCAAACAACCAGATAATTAATTATCGATGTGACCCTACAGAAAAATGGTTGGTTTT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------gttt-tatatcttt---aacttactgtcagcttcttcatatcatgtatatgt-tgtttctcatttttgcttcgatatttccagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGCAAACAATCAAATTATAAACTATAAGTGCTCTCCTAATGAGAAGTGGTTGGTCTT
||| |||| || | | || || |||| || || | | || | |||| | || | || |||||| ||||| || |||||||||||||| ||||| || |||||||||||||| || || || || ||| || |||| || || |||||||||||
gtaagatgataatttgctcaactaaatatttttgtgttatactatattttccagttcacatattctttacagtgtgcttgtagtttctgcaaattgttgactggtacatggttcatgat--ctatataacttgtagGTGACTCTGAACCTGTTAAGATGTTTGAGAGAACAGCAAATTTGGCAAACAACCAGATAATTAATTATCGATGTGACCCTACAGAAAAATGGTTGGTCTT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 4
---------------------------------------gttttata----tctttaacttactgtcagcttcttcatatcat---gtatatgttgtttctcatttttgcttc--gatatttccagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGCAAACAATCAAATTATAAACTATAAGTGCTCTCCTAATGAGAAGTGGTTGGTCTT
||||| | | | | ||| ||| | | | || | || | | | | |||| | | || |||||| ||||| || || ||||||||||| ||||| || |||||||||||||| ||||| || || |||| || |||| ||| || |||||||||||
gtaagacaatgataaactgcaattctgcttaactacatggttttgtgctgttttccagtttatgcattgctgttcagtgttattttgctcatcagtatatttgtctgtgctatatgtaacttgtagGTGACTCTGAACCTGTAAAGATGTTTGAGAGAACAGCGAATTTGGCAAACAACCAAATAATTAATTATAGATGTGATCCTTCTGAAAAATGGTTGGTCTT
upper sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 4
gttttatatctttaacttactgtcagcttcttcatatcatgtatatgttgtttctcatttttgcttcgatatttccagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGCAAACAATCAAATTATAAACTATAAGTGCTCTCCTAATGAGAAGTGGTTGGTCTT
|| || | | || || | || ||| ||| ||| | ||||||||||||||| || ||| ||||||||||||||||||| || | ||||||||||| ||||| || |||| |||||||||| | || |
------------------------gtatttttaagaatttgcttacatca--actgattacagctacga-----ctagGTGATTCTGAGCCGGTCAAGGTGTTTGATAGAACGGCTAACCTGTCGGGAAATCAAATTATTAACTACCGCTGTGATCCTTCTGAGAAGTGGCTAGTTCTMapped 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|19877198|gb|AU238029.1|AU238029EST: GATGCTGGGACTGGTCACACAAACTTCTGTGNATCATTGGTCAATTGAAG GNGATTCTGAGCCAGTTAAGANGTT-GATAGAACGGCTAATTTGGC
genomic: GATGCTGGGACTGGTCACACAAACTTCTGTGTATCATTGGTCAATTGAAGgttttatatc ... atatttccagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagcttcttcatatcatgtatatgttgtttctcatttttgcttcgatatttccagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGCAAACAATCAAATTATAAACTATAAGTGCTCTCCTAATGAGAAGTGGTTGGTCTT
tatttcc CT-rich tract
atgtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttatatctttaacttactgtcagcttcttcatatcatgtatatgttgtttctcatttttgcttcgatatttccagGTGATTCTGAGCCAGTTAAGATGTTTGATAGAACGGCTAATTTGGCAAACAATCAAATTATAAACTATAAGTGCTCTCCTAATGAGAAGTGGTTGGTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT