Sequence
atgc intronic sequence ATGC exonic sequencegtaatttaatggagtctcaagtctcaatctatcctttgttcgcttattgtttcgttgaaatatttttgttttgttttgttactctttagTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTCCAGAAACTGCTACTGTTGGCTCCTTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G46590.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G46590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g16700.4 (Oryza sativa), 3'ss of exon 4
gtaa-tttaatggagtctcaagtctcaatctatcctttgttcgcttattgtttcgttgaaatatttttgttttgttt-tgttactcttt--agTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTCCAGAAACTGCTACTGTTGGCTCCTTGAAG
|||| ||| | || | | | || | | | || | |||| | | ||| | | || | | || ||| || ||| || || ||||||||||||| | ||||||||| ||| | | ||||| ||||||||||| |||||||| || |||||
gtaagtttggccccatgaaaaatgttt-ttgatattgtaattattt-tggttttatggccatagtctaagactgcctgtttttctccttgcagTAAAACTTAGGATCAAGTCTTTCAAGGTGCCTGAACTTCTAATTGAGATCCCAGAAACTGCGACTGTTGGTTCACTGAAG
upper sequence: AT3G46590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G14760.4 (Glycine max), 3'ss of exon 4
------gtaatttaatggagtctcaagtctcaatctatcctttg--ttcgcttattgtttcgttgaaatatttttgttt---tgttttgttactctttagTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTCCAGAAACTGCTACTGTTGGCTCCTTGAAG
| | || | |||| ||| ||| || ||| ||||| || || ||| | | || | | ||| || | | |||||| || |||||||||| ||||| ||||| |||||||| ||||| ||||||||||||| || |||| |||||||||
gtatgagaagattgagggag---caattctttatgtattctttgacttgatcgatatcttcaaaggggttcttacatgtaaatgtctttcttttaaccagTGAATCTTAGGATCAAGTCATTTAGAGTGCCAGAGCTTTTTATAGAGGTTCCAGAAACTGCAACAATTGGGTCCTTGAAG
upper sequence: AT3G46590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G06680.1 (Glycine max), 3'ss of exon 4
------gtaatttaatggagtctcaagtctcaatctatcctttg-ttcgcttattgt-ttcgttgaaatatttttgttt---tgttttgttactctttagTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTCCAGAAACTGCTACTGTTGGCTCCTTGAAG
| | || | |||| ||| ||| || ||| ||||| || | | | | | ||| | | | | | ||| || | | |||||| || |||||||||| ||||| ||||| |||||||| ||||| ||||||||||||| || |||| |||||||||
gtatgagaagattgagggag---caattctttatgtattctttgatttgatcaatatcttcaaaggagttctcacatgcaaatgtctttcttttaaccagTGAATCTTAGGATCAAGTCATTTAGAGTGCCAGAGCTTTTTATAGAGGTTCCAGAAACTGCAACAATTGGGTCCTTGAAG
upper sequence: AT3G46590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G04200.1 (Glycine max), 3'ss of exon 5
------gtaatttaatggagtctcaagtctcaatctatcctttg--ttcgcttattgtttcgttgaaatatttttgttttgttttgttactctt---tagTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTCCAGAAACTGCTACTGTTGGCTCCTTGAAG
| | || | ||||| | ||| || || ||||| || || || ||| | | || | | | | || || || ||||||||| ||||||| || || || |||||||||||||| | ||||||||||||||||| || || || ||| |||||
gtatgggaagattgagggagt---gattctttatgtactctttgatttgactgatgtcttcaaaggggttcttacatgaagatgtctttcttttaaccagTGAAGCTTAGGATCAAATCATTCAGAGTGCCTGAGCTTTTTATCGAGATTCCAGAAACTGCAACCGTCGGGTCCCTGAAG
upper sequence: AT3G46590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G41210.1 (Glycine max), 3'ss of exon 7
--------------------------------------------gtaatttaatggagtctcaagtctcaatctatcctttg--ttcgcttattgtttcgttgaaatatttttgt---tttgttttgttactctttagTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTCCAGAAACTGCTACTGTTGGCTCCTTGAAG
| | || | ||| | | ||| || || ||||| || || || ||| | | || | ||| || | | | ||||||||| ||||||| || ||||| ||||| |||||||| | ||||||||||||||||| ||
cttgggacactctgcattacgatctagagattcttacggtatgggaagattgagggaat---gattctttatgtactctttgatttgactgatgtcttcaaagGGGTTCTTACATGGAGATGTCTTTCTTTTATCCAGTGAAGCTTAGGATCAAATCATTTAGAGTGCCCGAGCTTTTTATCGAGATTCCAGAAACTGCAACC---------------
upper sequence: AT3G46590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 5
-------gtaatttaatggagtctcaagtctcaatctatcctttg-ttcgcttattgtttcgt---tgaaatatttttgttttgttttgttactcttta----gTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTCCAGAAACTGCTACTGTTGGCTCCTTGAAG
||| ||||||| | ||| | || |||| | | || ||| | | ||| | || ||| | | | || | |||| |||||||| ||||||||||||| |||||||| ||||| || ||||||||||||||||||| |||||||| ||| | |||
gtatgagagcctttgatggagt---gattcttatgtactcttttgacttgattggtgtctgatattcgaagttcttatgtgaagatgtatttccttttactcagTGAAGCTTAGGATCAAGTCTTTCAGGGTGCCAGAGCTCTTTATAGAGATTCCAGAAACTGCAACTGTTGGTTCCCTCAAGMapped 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|164192926|gb|EL986976.1|EL986976EST: GCGTCCTTTGTGTCAAGGGATCATCATG TGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTT-CGTAGAGATTC
genomic: GCGTCCTTTGTGTCAAGGGATCATCATGgtaatttaat ... tactctttagTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTC
EST:
gi|164222026|gb|EL978072.1|EL978072EST: GCGTCCTTTGTGTCAAGGGATCATCATG TGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTC
genomic: GCGTCCTTTGTGTCAAGGGATCATCATGgtaatttaat ... tactctttagTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttcgcttattgtttcgttgaaatatttttgttttgttttgttactctttagTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTCCAGAAACTGCTACTGTTGGCTCCTTGAAG
ttttgttactcttt CT-rich tract
ttgaaatatttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttaatggagtctcaagtctcaatctatcctttgttcgcttattgtttcgttgaaatatttttgttttgttttgttactctttagTGAAGCTGCGGATCAAGTCTTTTAGGGTGCCTGAGCTTTTCGTAGAGATTCCAGAAACTGCTACTGTTGGCTCCTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG