Sequence
atgc intronic sequence ATGC exonic sequencegtaaggtaacatggtaaaccatctttcaagatcaacattgatgagtgattaaggtactctatcaactgaattatcattttgtttcagGCATATGTTTATTTGGACGAAGCTCATAGCATTGGAGCAATTGGCAAAACAGGACGAGGTGTTTGTGAACTCCTAGGAGTTGACACTACTGAAGTGGACA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48790.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G26210.1 (Glycine max), 3'ss of exon 7
-----gtaaggtaacatgg-taaaccatc--tttcaagatcaacattgatgagtgattaaggtactctatca---actgaattat--cattttgtttcagGCATATGTTTATTTGGACGAAGCTCATAGCATTGGAGCAATTGGCAAAACAGGACGAGGTGTTTGTGAACTCCTAGGAGTTGACACTACTGAAGTGGACA
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acattaagggggattttggatgaactttttattataaagttctattttccattttactttggttcattgttactttctgtattttttcattgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGACAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA
upper sequence: AT3G48790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 7
-----gtaaggtaacatggtaaaccatctttca--agatcaacattgatgagtgattaaggtactctatcaactgaattat------cattttgtttcagGCATATGTTTATTTGGACGAAGCTCATAGCATTGGAGCAATTGGCAAAACAGGACGAGGTGTTTGTGAACTCCTAGGAGTTGACACTACTGAAGTGGACA
|| || ||||| | | | | | | || | | | ||| | | | | | ||| |||| || |||| ||| |||||||||||||| || ||||||||||| | ||||| ||||| ||||||||||||| ||| | || || || ||| |||| || ||||
cattaagggggatttttgataaactttttattatgaagttttattttccattttactttggttcattgttactttgtgtattttttccattgctttatagGCTTATACATATTTGGACGAAGCACACAGCATTGGAGCTGTGGGCAAGTCAGGAAGAGGTGTTTGTGAGCTCTTGGGTGTGGATACTGCTGATGTTGACA
upper sequence: AT3G48790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 8
---------------gtaaggtaacatggtaaaccatctttcaagatcaacattgatgagtgattaaggtactctatcaactgaattatcattttgtttcagGCATATGTTTATTTGGACGAAGCTCATAGCATTGGAGCAATTGGCAAAACAGGACGAGGTGTTTGTGAACTCCTAGGAGTTGACACTACTGAAGTGGACA
| | | | | | | || | | ||| || || | | || | | || | || || |||| || | ||||||||||||| ||||| || || || || ||||||||| |||| ||||||||| ||||||| ||||| ||| |||| || || || |||| ||||| |
agctctgttttctctttgatgcatcttaacttagggcctct-attttcatttttcataaatatttttgtttgtcatttttctatctttctatttggtgt-agGCATATGTTTACTTGGATGAGGCACACAGTATTGGAGCAGTTGGGAAAACAGGAAGAGGTGTCTGTGAGCTCTTAGGTGTGGATACCGCTGATGTGGATA
upper sequence: AT3G48790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0068g01300.t01 (Vitis vinifera), 3'ss of exon 7
---------gtaaggtaacatggtaaaccatctttcaagatcaacattgatgagtgattaaggtactct-----atcaactgaattatcattttgtttcagGCATATGTTTATTTGGACGAAGCTCATAGCATTGGAGCAATTGGCAAAACAGGACGAGGTGTTTGTGAACTCCTAGGAGTTGACACTACTGAAGTGGACA
| | || | ||||| | | || || | || ||| ||| | |||| |||||||| |||||||| || || || ||||| || ||| |||| ||||||||| ||||||||||||| ||| ||||||| || || |||| ||||| |
ttttcgttgctttttctatgtgaatagttctctttgtctctttcctttccgccccccccccctctcttttgagcattcactacatt-caaccctgttgtagGCATATTCCTATTTGGATGAGGCCCACAGCATAGGTGCAGTTGGGAAAACAGGAAGAGGTGTTTGTGAGCTCTTAGGAGTGGATCCTGCTGATGTGGATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caacattgatgagtgattaaggtactctatcaactgaattatcattttgtttcagGCATATGTTTATTTGGACGAAGCTCATAGCATTGGAGCAATTGGCAAAACAGGACGAGGTGTTTGTGAACTCCTAGGAGTTGACACTACTGAAGTGGACA
cattgat putative branch site (score: 4)
ttttgtttc putative PPT
aattatcattttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggtaacatggtaaaccatctttcaagatcaacattgatgagtgattaaggtactctatcaactgaattatcattttgtttcagGCATATGTTTATTTGGACGAAGCTCATAGCATTGGAGCAATTGGCAAAACAGGACGAGGTGTTTGTGAACTCCTAGGAGTTGACACTACTGAAGTGGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA