Sequence
atgc intronic sequence ATGC exonic sequence...agttcgtttttaagtaggttaagttgaaacatgaatcaattttggcgtcatgactcttgccttctctaagtttaaaataaagtttgttgctttgtaacagTCGTTGCACTAGTATTTCTTGGGTGCCTGGAGGTGATGGAGCATTTGTCGTTGCTCATGCCGATGGCAATTTGTATGTGTATGAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53390.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 5
-agttcgtttttaagtaggttaagttgaaacatg-aatcaattttggcgtcatgactcttgccttc--tctaagtttaaaataaagtttgttgctttgtaacagTCGTTGCACTAGTATTTCTTGGGTGCCTGGAGGTGATGGAGCATTTGTCGTTGCTCATGCCGATGGCAATTTGTATGTGTATGAGAAG
| | || || ||||| ||| | || ||| | | |||| | ||| | ||| | | | | ||| ||||||| || ||||||||| ||| ||||| ||||||||||||||||||||| || ||||| || |||||||| ||||| |||||||||
taaaaatgtccaaattatgttaaagatctttatgcattccattattgtgtcaaggacactgcatggaaactagctctgattcatgcttttttgcttt-tagCAGTCGTTGTACTTGTATTGCTTGGGTGCCTGGAGGTGATGCTGCCTTTGTTGTAGCTCATGCTGATGGGAATTTGTAT------------
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 5
-agttcgtttttaagtaggttaagttgaaacatgaatcaattttggcgtcatgactcttgccttctctaagtttaaaataaagtttgttgctttgtaacagTCGTTGCACTAGTATTTCTTGGGTGCCTGGAGGTGATGGAGCATTTGTCGTTGCTCATGCCGATGGCAATTTGTATGTGTATGAGAAG
| || ||| | || || | || | | | ||| | | |||| | | ||| | | | | ||| |||||||| | ||||| ||| ||| ||||| ||||||| |||||||||||||| || ||||| || | |||||| ||||| |||||||||
aaatttgttgtgttataaaaaaatgtccaaaagcatttgattatcgagtcaaggacactatgcaaactagctctgattgatgcttttttgctttg-agcagTCATTGTACTTGTATTGCTTGGGTTCCTGGAGGTGATGGTGCCTTTGTTGTAGGTCATGCTGATGGGAATTTGTAT------------
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G33740.1 (Glycine max), 3'ss of exon 4
agttcgtttttaagtaggttaagt--tgaaacatgaatcaattttggcgtcatgactcttgccttctctaa-----gtttaaaataaagtttgttgctttgtaacagTCGTTGCACTAGTATTTCTTGGGTGCCTGGAGGTGATGGAGCATTTGTCGTTGCTCATGCCGATGGCAATTTGTATGTGTATGAGAAG
|| ||| ||| | | ||| | ||| ||| | ||| | | || | | | | || | | || | ||| || ||||||||||| ||| ||||| | |||||||||||||||||||| | ||||| ||| |||| | ||||| ||||||||||| || || |||
------gaattgcttagcttacattctagaactttaatgtattggaatggtatgtcaatggcactgattggaacctatcttaattgatgtattttgaatt-caacagTCGTTGTACTTGTATTGCATGGGTGCCTGGAGGTGATGGTTCTTTTGTTGTTTCTCACACTGATGGGAATTTGTATGTATACGAAAAG
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G36480.1 (Glycine max), 3'ss of exon 4
-agttcgtttttaagtaggttaagttgaaacatgaatcaattttggcgtcatgactcttgccttctctaagtttaaaataaagtttgttgctttgtaacagTCGTTGCACTAGTATTTCTTGGGTGCCTGGAGGTGATGGAGCATTTGTCGTTGCTCATGCCGATGGCAATTTGTATGTGTATGAGAAG----
||| | | || | | | || | ||| ||| | || || | | | || | | || | || || ||||||||||| ||| ||||| ||||||| |||||||| ||||| | || || ||| ||||||| ||||| |||||||| || ||||| |||
gagtattctctgaattgttacattctataaatttaatgtattggaatgccaaagacagtgattggaacctatcttaattgatgtattttcaatt-caacagTCGTTGTACTTGTATTGCTTGGGTTCCTGGAGGCGATGGTTCTTTCGTTGTTTCTCATGCTGATGGGAATTTGTACGTATATGAAAAGGCAA
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 3'ss of exon 4
----agttcg--tttttaagtaggttaagttgaaacatgaatcaattttggcgtcatgactcttgccttctctaagtttaaaataaagtttgttgctttgtaacagTCGTTGCACTAGTATTTCTTGGGTGCCTGGAGGTGATGGAGCATTTGTCGTTGCTCATGCCGATGGCAATTTGTATGTGTATGAGAAG
| | | ||| | | || |||| | || ||| | | | | || | |||| ||| || || ||| ||| ||| || ||||| ||||| ||| | ||||| |||| |||||||| || || || ||||||||||| ||||| |||||||| ||||||||||||
tctgaataaggactttcagatgcattcagttccatgcaagtagaagtttaatatttagttagtaggtttaaccaagt--aaacta---cttcttgtttt-taatagCCGTTGTACTAGCATTGCATGGGTCCCTGATGGTGATGGTGCTTTCGTTGTTGCTCATGCTGATGGAAATTTGTACGTGTATGAGAAGMapped 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|164149880|gb|ES044050.1|ES044050EST: AAGCTAGTTGGTGCTCTGCATTATAACAAGGACGGTTCTGTGAATAACAG TCGTTGCACTAGTGTTTCTTGGGTGCCTGGAGGTGAT
genomic: AAGCTAGTTGGTGCTCTGCATTATAACAAGGACGGTTCTGTGAATAACAGgcaagagttt ... tttgtaacagTCGTTGCACTAGTATTTCTTGGGTGCCTGGAGGTGAT
EST:
gi|164040436|gb|ES146017.1|ES146017EST: AAGCTAGTTGGTGCTCTGCATTATAACAAGGACGGTTCTGTGAATAACAG TCGTTGCACTAGTTGTTTCTTGGGTGCCTGGAGGTGAT
genomic: AAGCTAGTTGGTGCTCTGCATTATAACAAGGACGGTTCTGTGAATAACAGgcaagagttt ... tttgtaacagTCGTTGCACTAGTA-TTTCTTGGGTGCCTGGAGGTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtcatgactcttgccttctctaagtttaaaataaagtttgttgctttgtaacagTCGTTGCACTAGTATTTCTTGGGTGCCTGGAGGTGATGGAGCATTTGTCGTTGCTCATGCCGATGGCAATTTGTATGTGTATGAGAAG
ttgcttt CT-rich tract
taagtttaaaataaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttcgtttttaagtaggttaagttgaaacatgaatcaattttggcgtcatgactcttgccttctctaagtttaaaataaagtttgttgctttgtaacagTCGTTGCACTAGTATTTCTTGGGTGCCTGGAGGTGATGGAGCATTTGTCGTTGCTCATGCCGATGGCAATTTGTATGTGTATGAGAAG
- - - - - - - - - - - - -gaaacat
- - - - - - - - - - - - - - - - gaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa