Sequence
atgc intronic sequence ATGC exonic sequence...gcttgtttgtttgtaagttagacctggtttatttgtttgtagttattttccctttttaaaaaaccttactgggaactggtttattctgcaacattctcagGGCTGGAAACTTCCGGATCTTATGTTTGCAACAAGGCGCAGCTTATCAGATGCATGTAATAGTGTTGGCAGCCAGATCGATGGTTTTTACACATCACTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G24267.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G24267.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G29150.3 (Glycine max), 3'ss of exon 5
gcttgtttgtttgtaagttagacctggtttatttgtttgtagttattttccctttttaaaaaaccttactgggaactggtttat---tctgcaacattctcagGGCTGGAAACTTCCGGATCTTATGTTTGCAACAAGGCGCAGCTTATCAGATGCATGTAATAGTGTTGGCAGCCAGATCGATGGTTTTTACACATCACTCT
| || ||| | | | | | | | | ||| | || | | || || | | ||||| ||| || ||||| ||||| ||||| ||||| ||||||||||||||||| | || || ||||| || | | |||| | ||||| | |||| |||| |
---taattttttattaaatgattttcttactataatcttaccttactatctccaactttaattttttttaaatgatttttttatggctcttgtgtgtttgcagGGATGGAAGCTTCCTGATCTGATGTTTGCAACAAGGCGTGGTTTGTCTGATGCTTGCACATCTATTGGTAATCAGATGGGAAAGCTTTATGAATCAATTG
upper sequence: AT1G24267.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G52020.1 (Glycine max), 3'ss of exon 5
gcttgtttgtttgtaagttagacctggtttatttgtttgtagttattttccctttttaaaaaaccttact-----gggaactggttt----attctgcaacattctcagGGCTGGAAACTTCCGGATCTTATGTTTGCAACAAGGCGCAGCTTATCAGATGCATGTAATAGTGTTGGCAGCCAGATCGATGGTTTTTACACATCACTCT
| ||| || | | | ||||| | || ||| | | | || || ||| ||| ||| |||| ||| | || ||||| ||||| ||||| ||||| ||||||||||||||||| | || || ||||| || | |||| | ||||| | |||| |||| |
-------tttttaaaaatgaattttcttttatctcaccata-ctatctccaaatcttcaactaccccactctcttatgaatgagttttatggctcttgtgcgtttgcaGGGATGGAAGCTTCCTGATCTGATGTTTGCAACAAGGCGTGGTTTGTCTGATGCTTGCACATCAATTGGTAATCAGATGGGAAAGCTTTATGAATCAATT-
upper sequence: AT1G24267.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0010g03920.t01 (Vitis vinifera), 3'ss of exon 5
gcttgtttgtttgtaagttagacctggtttatttgtttgtagttattttccctttttaaaaaaccttactggg-aactggtttatt--ctgcaacatt---ctcagGGCTGGAAACTTCCGGATCTTATGTTTGCAACAAGGCGCAGCTTATCAGATGCATGTAATAGTGTTGGCAGCCAGATCGATGGTTTTTACACATCACTCT
|||| | || | | | ||| | || || | | | || || || | ||| | | | |||||| || | |||||||||| ||||| ||| | ||||||||||| ||||| || ||||||||||| || | ||| | ||| | || | |||| ||||| |
----gtttactgtcaaaccaaatcatatttcaataagagtg--catgataacgcctaaatgtttatttgtgattagctgatcgactaattgcaactttgaatttagGGCTGGAAGCTTCCTGATATGATGTTTGCAACGAGGCGTAGTTTATCAGATGCTTGCTCTTCAATTGCTAAACAGCTTGAGAATGTTTATTCATCAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttccctttttaaaaaaccttactgggaactggtttattctgcaacattctcagGGCTGGAAACTTCCGGATCTTATGTTTGCAACAAGGCGCAGCTTATCAGATGCATGTAATAGTGTTGGCAGCCAGATCGATGGTTTTTACACATCACTCT
accttac putative branch site (score: 3)
cattctc putative PPT
tttttaaaaaacctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttgtttgtttgtaagttagacctggtttatttgtttgtagttattttccctttttaaaaaaccttactgggaactggtttattctgcaacattctcagGGCTGGAAACTTCCGGATCTTATGTTTGCAACAAGGCGCAGCTTATCAGATGCATGTAATAGTGTTGGCAGCCAGATCGATGGTTTTTACACATCACTCT
- -tgtttgt
- - - - - - - - - - - - -ggtttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaac