Sequence
atgc intronic sequence ATGC exonic sequence...gctccttttctgagtgctaatcaacataaattgttcatttttttgggatgaattattcgaagtaattgcgtgagaagtttagctgctttgcattttttagGAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACATACTGCAAGGCAAGAGCTAAGTCATGCCTTGTATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G33340.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G33340.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G21330.1 (Glycine max), 3'ss of exon 4
gctccttttctgagtgctaatcaacataaattgttcatttttttgggatgaattat--tcgaagtaattgcgtgagaagtttagctgctttgcattttttagGAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACATACTGCAAGGCAAGAGCTAAGTCATGCCTTGTATCAG
||| |||| | | | | ||| || | ||| | || || | | | || | ||| | || | | | | ||| ||||||||||| || ||||||||||| ||||||||| ||||||||||| | || || ||||| |||||||| |||||||| |||||||||
-aaatatttagacatgcttagatatgtgtaggcttctttctgttgaaaaaaacaattatttaggcttccgcataagatgatttggt-ttgcctaatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAAGAGCTGAGTCATGCTTTGTATCAG
upper sequence: AT2G33340.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G26870.1 (Glycine max), 3'ss of exon 4
gctccttttctgagtgctaatcaacataaattgttcatttttttgggatgaattat--tcgaagtaattgcgtgagaagtttagctgctttgcattttttagGAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACATACTGCAAGGCAAGAGCTAAGTCATGCCTTGTATCAG
||| |||| | | | | ||| || | ||| | | | || | | | | ||||| | || | | | | ||| ||||||||||| || ||||||||||| ||||||||| ||||||||||| | || || ||||| || ||||| |||||||| ||||||||
-aaatatttagacatgcttagatgtgtgtagtcttctttctgttgaaaaaagtaattatttaggcttccacttgagatgatttggt-ttgcctaatttgtagGAATGGGATGGATTGATGCTATCTAATTTTGCATTGGAGCAACAATTGCACACAGCAAGACAGGAGCTGAGTCATGCTCTGTATCAG
upper sequence: AT2G33340.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0049g01840.t01 (Vitis vinifera), 3'ss of exon 4
--gctccttttctgagtgctaatcaaca-taaattgttcatttttttgggatgaattattcgaagtaattgcgtgagaagtttagctgctttgcattttttagGAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACATACTGCAAGGCAAGAGCTAAGTCATGCCTTGTATCAG
| | | | | || || | |||||| ||||| ||| | | | || || | | ||| | ||| || | ||||||||||| || ||||||||||| |||||||| ||||||||||||| |||||||| ||||| |||||||||||||| ||||| |||
atgttgttagttatggcattagattgcacttcattgttaatttt--aaagattctctcattttaatatttaag-gccttttttttttctttttcaaataatagGAATGGGATGGCTTGATGCTATCCAATTTTGCGTTGGAGCAACAACTGCATACTGCTAGGCAGGAGCTAAGTCATGCTTTGTACCAGMapped 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|116444558|gb|EG487150.1|EG487150EST: AAACATTGCATACAGCTAGTATCCCTGGATTGCTCGGAACGTTCCAGAAT GAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACAT
genomic: AAACATTGCATACAGCTAGTATCCCTGGATTGCTCGGAACGTTCCAGAATgtaagcttta ... cattttttagGAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACAT
EST:
gi|116472806|gb|EG515398.1|EG515398EST: AAACATTGCATACAGCTAGTATCCCTGGATTGCTCGGAACGTTCCAGAAT GAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACAT
genomic: AAACATTGCATACAGCTAGTATCCCTGGATTGCTCGGAACGTTCCAGAATgtaagcttta ... cattttttagGAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatgaattattcgaagtaattgcgtgagaagtttagctgctttgcattttttagGAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACATACTGCAAGGCAAGAGCTAAGTCATGCCTTGTATCAG
catttttt CT-rich tract
atttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctccttttctgagtgctaatcaacataaattgttcatttttttgggatgaattattcgaagtaattgcgtgagaagtttagctgctttgcattttttagGAATGGGACGGTTTGATGCTATCAAATTTTGCACTGGAGCAACAACTACATACTGCAAGGCAAGAGCTAAGTCATGCCTTGTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT