Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttttctcgttacctctgctaagtctaatcattttgttccaaagtatctgggaaaaggaaggctcattcatgccatgactgctagGTCGCTGTATATGCAGAGTTTCGTAGAGATTGGGGTGAAGCACTGAAGTTTTATGAAGACGCATACCATTCCTTGCACGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65950.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G21610.1 (Glycine max), 3'ss of exon 3
gtaagcttttct---cgttacctctgctaagtcta-atcattt-tgttccaaagtatctgggaaaaggaag--gctcattca--tgccatga-ctgctagGTCGCTGTATATGCAGAGTTTCGTAGAGATTGGGGTGAAGCACTGAAGTTTTATGAAGACGCATACCATTCCTTGCACGAG
||| |||| | || | || || ||| | | ||| |||| | | | || | | | ||| | |||||||| |||||||| |||||||||||||| || || || |||||| ||||||| |||| |||||||| || || || ||| | ||| |||
gtaccctttgttgttcgggaacttgtctgagtttgtgttgtttatgtttttatcaaaataaaaattgtacattatttatttagatgccatgaattgctagGTTGCTGTATATGCAGAATTCCGAAGTGATTGGACTGAAGCAATGAAATTTTATGAGGAGGCCTATCATACACTGCGAGAG
upper sequence: AT5G65950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G32860.1 (Glycine max), 3'ss of exon 3
----gtaagcttttctcgttacctctgctaagtctaatcattt-tgttccaaagtatctgggaa--aaggaaggctcattca--tgccatga-ctgctagGTCGCTGTATATGCAGAGTTTCGTAGAGATTGGGGTGAAGCACTGAAGTTTTATGAAGACGCATACCATTCCTTGCACGAG
| | | || | || | || | ||| |||| | | | || | | | ||| | |||||||| |||||||| |||||||||||||| || || || || ||| |||||||||||| |||||||| || || || ||| | ||| |||
ttgtgccatttgttgttcggggacttgtgaggttgcgttgtttatgtttttatcaaaataaaaattgtgcattatttatttagatgccatgaattgctagGTTGCTGTATATGCAGAATTCCGAAGTGACTGGACTGAAGCACTGAAATTTTATGAGGAGGCCTATCATACACTGCGAGAG
upper sequence: AT5G65950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0044g01720.t01 (Vitis vinifera), 3'ss of exon 4
-gtaagcttttctcgttacctctgctaagtctaatcattttgt---tccaaagtatctg----ggaaaaggaaggctcattcatgccatg---actgctagGTCGCTGTATATGCAGAGTTTCGTAGAGATTGGGGTGAAGCACTGAAGTTTTATGAAGACGCATACCATTCCTTGCACGAG
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tatttcctattatcaatgcatagactctgtc-aattattctaaatgttgcatgtgttttctctggttggtcattatttatctaaactctatgaattgctagGTTGCTGTATATGCAGAATTTCGAAGAGACTGGGCTGAAGCTTTGAGGTTTTATGAAGATGCATATCACACACTGCGAGAGMapped 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|116396088|gb|EG438680.1|EG438680EST: AGAAAAGGAGTTCCAATTCTCTTGATTTGAATGTTCGCTACTGTTTTAAA GTCGCTGTATATGCAGAGTTTCGTAGAGATTGGGGTGAAGCACTGAAG
genomic: AGAAAAGGAGTTCCAATTCTCTTGATTTGAATGTTCGCTACTGTTTTAAAgtaagctttt ... tgactgctagGTCGCTGTATATGCAGAGTTTCGTAGAGATTGGGGTGAAGCACTGAAG
EST:
gi|116416782|gb|EG459374.1|EG459374EST: AGAAAAGGAGTTCCAATTCTCTTGATTTGAATGTTCGCTACTGTTTTAAA GTCGCTGTATATGCAGAGTTTCGTAGAGATTGGGGTGAAGCACTGAAGTTT
genomic: AGAAAAGGAGTTCCAATTCTCTTGATTTGAATGTTCGCTACTGTTTTAAAgtaagctttt ... tgactgctagGTCGCTGTATATGCAGAGTTTCGTAGAGATTGGGGTGAAGCACTGAAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgttccaaagtatctgggaaaaggaaggctcattcatgccatgactgctagGTCGCTGTATATGCAGAGTTTCGTAGAGATTGGGGTGAAGCACTGAAGTTTTATGAAGACGCATACCATTCCTTGCACGAG
aaagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttttctcgttacctctgctaagtctaatcattttgttccaaagtatctgggaaaaggaaggctcattcatgccatgactgctagGTCGCTGTATATGCAGAGTTTCGTAGAGATTGGGGTGAAGCACTGAAGTTTTATGAAGACGCATACCATTCCTTGCACGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA