Sequence
atgc intronic sequence ATGC exonic sequence...cgaagaagccattggatatgtacttggacttagtttgcttactgcgtagtttgagatttatataagagttagttatttttgtgcttttgtgttgatgcagAAGGCATATTTCAAATGTGCATACGAGTGCTTTGATAGGACAAGAACACACGCTGAGATTAGTCGATGTGCAGAGAGTTGCAGTGTTCCTATCACAAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G43720.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G43720.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G06480.3 (Glycine max), 3'ss of exon 2
---cgaagaagccattggatatgtacttggacttagtttgcttactgcgtagtttgagatttatataagagttagttatttttgtgcttttgtgttgatgcagAAGGCATATTTCAAATGTGCATACGAGTGCTTTGATAGGACAAGAACACACGCTGAGATTAGTCGATGTGCAGAGAGTTGCAGTGTTCCTATCACAAATG
| ||| || ||| || | | | ||||| | || | || | ||||| || | || || | | ||||||| |||||||| || |||||||| |||||||||||||| | | || || | || || || | |||| || | ||||||| ||||| | | ||||
atattagttttgcatacaattggtatatgtggt-aatgtgcttgtttgataaagcagacatccaattccatgtagttgattgtttgattgaataat--tgcagAAAGCATATTTTAAGTGTGCATATGAGTGCTTTGATAGAAGCAAAAGGCAGGAAGAAATAAGCAGTTGTGTCGAAAATTGCAGTATTCCTCTTTCTAATG
upper sequence: AT2G43720.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G47800.1 (Glycine max), 3'ss of exon 2
---cgaagaagccattggatatgtacttggacttagtttgcttactgcgtagtttgagatttatataagagttagttatttttgtgcttttgtgttgatgcagAAGGCATATTTCAAATGTGCATACGAGTGCTTTGATAGGACAAGAACACACGCTGAGATTAGTCGATGTGCAGAGAGTTGCAGTGTTCCTATCACAAATG
| ||| || ||| || | | | ||||| | || | || | ||||| || | || || | | | ||||| |||||||| || |||||||| |||||||||||||| | | || || | || || || | |||| || | |||||| ||||| | | ||||
atattagttttgcatacaattggtatatgtggt-aatgtgcttgtttgataaagcagacatccaattccatgtagttgattgtttgattgaataat--tacagAAAGCATATTTTAAGTGTGCATATGAGTGCTTTGATAGAAGCAAAAGGCAGGAAGAAATAAGCAGTTGTGTCGAAAATTGCAGCATTCCTCTTTCTAATG
upper sequence: AT2G43720.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0077g02200.t01 (Vitis vinifera), 3'ss of exon 1
cgaagaagccattggatatgt----acttggacttagtttgctt-actgcgtagtttgagatttatataagagttagttatttttgtgcttttgtgttgatgcagAAGGCATATTTCAAATGTGCATACGAGTGCTTTGATAGGACAAGAACACACGCTGAGATTAGTCGATGTGCAGAGAGTTGCAGTGTTCCTATCACAAATG
| ||| |||| | ||||| || | | | | | || | | | | || |||| || | || | | | ||||| | ||||| |||||||| |||||||||||||| ||||||| ||||| || | || || || |||| || |||||||||||| | ||||
-----tactttttgaatatttgaccacttgttattgtctcttgtgattccatattgttcttcatgtgtataagtttgtctgaaatctgaatgagactgcttgcagCAAGCATACTTCAAATGCGCATACGAGTGCTTCGATAGGAAAAGAAAGCAAGAAGAAATAAGCAACTGTGTTGAACATTGCAGTGTTCCAGTTGTTAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagtttgagatttatataagagttagttatttttgtgcttttgtgttgatgcagAAGGCATATTTCAAATGTGCATACGAGTGCTTTGATAGGACAAGAACACACGCTGAGATTAGTCGATGTGCAGAGAGTTGCAGTGTTCCTATCACAAATG
tgttgat putative branch site (score: 4)
agatttatataagagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgaagaagccattggatatgtacttggacttagtttgcttactgcgtagtttgagatttatataagagttagttatttttgtgcttttgtgttgatgcagAAGGCATATTTCAAATGTGCATACGAGTGCTTTGATAGGACAAGAACACACGCTGAGATTAGTCGATGTGCAGAGAGTTGCAGTGTTCCTATCACAAATG
cgaagaa
- - - - - - - - - - - - - - - - - - - - - - - -agtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttttg