Sequence
atgc intronic sequence ATGC exonic sequencegtaaccaaaccctaacttaagctttaagtcaatgaagaaaacagttttttaacattgggtttttgaattctcagAGTGCGCAGAGGAAGGCTTTGGATGTTCTGAACACTGTTGGGCTCTCTAACTCTGTATTGAGGCTCATTGAGAGGCGTAATCGTGTTGATACCTGGATTA
Basic information
| species | Arabidopsis thaliana |
| transcript | AT5G50440.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g45260.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------gtaaccaaaccctaacttaagctttaagtcaatgaagaaaacagttttttaacattgg--gtttttgaattctcagAGTGCGCAGAGGAAGGCTTTGGATGTTCTGAACACTGTTGGGCTCTCTAACTCTGTATTGAGGCTCATTGAGAGGCGTAATCGTGTTGATACCTGGATTA
| || | |||| ||| | | | | | | || ||| | | | || || ||| |||||||| || ||||| || |||||| |||||||||| ||||| || || || ||||| |||| ||| ||||||||||| | ||||| || | ||||||
gtaaagcatatcccattaatcttcaccatgaaacatcagttttaacttgcatggttaatctt---cttagcttttgactgtctaattatttatgattgttattaatagtaattcctgcattg-cagAGTGCTCAAAGGAAAGCGTTGGATATTCTGAACACCGTTGGTCTATCAAATTCTGTTTTGAAGCTTATTGAGAGGCGGCACCGTGTGGACAAGTGGATTG
upper sequence: AT5G50440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G436429_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------gtaaccaaac----cctaacttaa-gctttaagtcaatgaagaaaacagttttttaacattgggtttttgaat---tctcagAGTGCGCAGAGGAAGGCTTTGGATGTTCTGAACACTGTTGGGCTCTCTAACTCTGTATTGAGGCTCATTGAGAGGCGTAATCGTGTTGATACCTGGATTA
| || ||| || | | ||| | | | |||| || || | || | | || | | | |||||||| || ||||| ||||||||||| ||||||||||| || || || ||||| || ||| || || |||||||| | || || || | |||||
gtaatgcatatcatccattcacgacgaagcctcggtttgaagttgaactgtggacagaagatcactgaacgtgaccaatcataatggctctttttaatggtctaacttgtgcctgctaatggccatcttcactgcattgcagAGTGCTCAAAGGAAAGCTTTGGATGTCCTGAACACTGTCGGTCTGTCAAACTCCGTTCTGAAACTTATCGAGAGGCGGCACCGCGTGGACAGGTGGATCG
upper sequence: AT5G50440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0056g01310.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtaaccaa--accctaacttaagctttaagtcaatgaagaaaacagttttttaacattgggtttttgaatt--ctcagAGTGCGCAGAGGAAGGCTTTGGATGTTCTGAACACTGTTGGGCTCTCTAACTCTGTATTGAGGCTCATTGAGAGGCGTAATCGTGTTGATACCTGGATTA
| || | | | ||| || ||||| || || |||| |||| | |||| || ||| | ||||| ||||| ||||||||||| || ||||| || ||| | || ||||| ||||||| ||| ||||||||||| || ||||| || | ||||| |
aactcctcaacccctcccttgtattttcatttgtttttattgcagcagtataccaatgctgatgacctttttgacacataacttctttgttttggtgcagGGAGCGCATAGGAAAGCTTTGGATGTCCTCAACACAGTGGGGTTGTCCAACTCGGTATTGAAGCTGATTGAGAGGCGGAACCGTGTGGACAAATGGATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctttaagtcaatgaagaaaacagttttttaacattgggtttttgaattctcagAGTGCGCAGAGGAAGGCTTTGGATGTTCTGAACACTGTTGGGCTCTCTAACTCTGTATTGAGGCTCATTGAGAGGCGTAATCGTGTTGATACCTGGATTA
ttttaac putative branch site (score: 2)
ttctc putative PPT
aaaacagttttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaccaaaccctaacttaagctttaagtcaatgaagaaaacagttttttaacattgggtttttgaattctcagAGTGCGCAGAGGAAGGCTTTGGATGTTCTGAACACTGTTGGGCTCTCTAACTCTGTATTGAGGCTCATTGAGAGGCGTAATCGTGTTGATACCTGGATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
