Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtcttcctcaatgttttcctcctgctgtacctaacatgccagctgtttcaatggtttaatcctcgtttctatttacgttttaattagGTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G24170.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G24170.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 7
gtaatgtcttcctcaatgttttcctcctgctgtacctaacatgccagctgtttcaatggtttaatcctcgtttctatttacgttttaattagGTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAG
||| | || || ||| | | | | || || | | | || | || | | || |||| | || |||||||| || ||||||||||| ||||||||||| |||||| | || || ||| || | ||||| ||||||||||| || ||
-------------gtgtgtatgtcttcttatgtgttttaagt-ttaactactt--agtatctcatggtgattaatttatattttttt-tcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGCATGGGTTCCACAGTTGATCTAGTTTTCAGAAAGGAACTTCCACTGAG
upper sequence: AT3G24170.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G08180.1 (Glycine max), 3'ss of exon 6
--gta-atgtcttcctcaatgttttcctcctgctgtacctaacatgccagctgtttcaatggtttaatcctcgtttctatttacgttttaattagGTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAG
|| |||||||| | |||||| | ||| || || || || || | ||| ||||| ||||| | || |||||||| || ||||||||||| ||||||||||| |||||| | || || ||| || | ||||| ||||||||||| || ||
gtgtgtatgtcttcttatgtgtttttagtttaac-tacttagtatctca-------tggtgattaa-------tttatattt-tgtttt--tcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGGATGGGTTCCACAGTTGATCTAGTTTTCAGAAAGGAACTTCCACTGAG
upper sequence: AT3G24170.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 8
gta-atgtcttcctcaatgttttcctcctg--ctgtacctaacatgccagctgtttcaatggtttaatcctcgtttctatttacgttttaattagGTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAG
|| | ||| |||| ||||||| || | | | | | || ||| ||| | ||| | || ||| | ||||||| |||||||| |||||||| ||||||||| ||| ||||||| | |||||||| |||| ||||| ||||||||||| ||||
gtgtgtttctacctcttcattttcctagtgtaccaagctcatcttattggcatgctcatgtttttggttgatattttt-ttcttgttct--ttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGTAGATCTATTTTTCAGAAAGGAACTTCCATTAAGMapped 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|116457529|gb|EG500121.1|EG500121EST: GCTTTGAGCTTGGAAGAATTTCCCAAGCGTGCTATAGTGCTTGGAGGAGG GTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGT
genomic: GCTTTGAGCTTGGAAGAATTTCCCAAGCGTGCTATAGTGCTTGGAGGAGGgtaatgtctt ... ttttaattagGTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGT
EST:
gi|164026979|gb|ES112049.1|ES112049EST: GCTTGGAAGAATTTCCCAAGCGTGCTATAGTGCTTGGAGGAGG GTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGT
genomic: GCTTGGAAGAATTTCCCAAGCGTGCTATAGTGCTTGGAGGAGGgtaatgtctt ... ttttaattagGTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatgccagctgtttcaatggtttaatcctcgtttctatttacgttttaattagGTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAG
tttctatttacgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtcttcctcaatgttttcctcctgctgtacctaacatgccagctgtttcaatggtttaatcctcgtttctatttacgttttaattagGTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA