Sequence
atgc intronic sequence ATGC exonic sequence...cacatagcgagaacgaagaaggtcgatgataggttaactaacctcaatcacgttctagttgattactatattcttctgtttgtgtaaatttatggcatagGTTGCACGTGGGAGCAAAGACACTGGAGAATCTATTCCCATGCTTTTGAGAATTCCACGGCTTTCTGATCCATGGGGTGGTTACAACATGATCGGTTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G05820.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G05820.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G44490.1 (Glycine max), 3'ss of exon 10
cacatagcgagaacgaagaaggtcgatgataggttaactaacctcaatcacgttctagttgattactatattcttctgtttgtgtaaatttatggcatagGTTGCACGTGGGAGCAAAGACACTGGAGAATCTATTCCCATGCTTTTGAGAATTCCACGGCTTTCTGATCCATGGGGTGGTTACAACATGATCGGTTTTG
| | | ||| || | | || | | | | | || | | | | | | ||| | | | ||| |||||||| ||||| ||| | | ||| ||| | ||||| |||||||||||| |||| || ||||||||||| |||||||| || | ||||| || ||||
cttgctataaatatttagatatacgtttttctttttcattctcactcctgagatttattacactgaaaaggtgtcctgaagttatgagtttcctttctagGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG
upper sequence: AT1G05820.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G39260.1 (Glycine max), 3'ss of exon 9
cacatagcgagaacgaagaaggtcgatgataggttaactaacctcaatcac--gttctagttgattactatattcttctgtttgtgtaaattta-tggcatagGTTGCACGTGGGAGCAAAGACACTGGAGAATCTATTCCCATGCTTTTGAGAATTCCACGGCTTTCTGATCCATGGGGTGGTTACAACATGATCGGTTTTG
| | ||| || | | | || | | |||| || ||| || | | | | ||| |||| | | | ||| | |||||||| ||||| ||| | | ||| ||| | ||||| |||||||||||| |||| || ||||||||||| |||||||| || | ||||| || ||||
--tgctataaatatttagatatacgttttttgtttttc-attctcactcctgagttttattatactgaaaaggtctcctgtagttatgagtttccttttctagGTTGCTCGTGGTGACAAGGCCGGTGGTGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTG
upper sequence: AT1G05820.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G47600.2 (Glycine max), 3'ss of exon 9
cacatagcgagaacgaagaaggtcgatgataggttaactaacctcaatcacgttctagttgat-tactatattcttctgtttgtgtaaatttatggcatagGTTGCACGTGGGAGCAAAGACACTGGAGAATCTATTCCCATGCTTTTGAGAATTCCACGGCTTTCTGATCCATGGGGTGGTTACAACATGATCGGTTTTG
| | | | | || | |||| | | | |||| ||| | || | | ||| | || | || |||||||| || || ||| | ||||||| | ||||| |||||||||||| |||| || |||| |||||| ||||| ||||| ||||||| || ||||
aatggattctgtgttttctataatgctgctttattaaaaaggaagagaga-attctggtttttatagttttttcatactcttacatgggctttctttttagGTTGCTCGAGGTGACAAGGCTGGTGGAGAAGCAATTCCTATGCTTTTGAGATTTCCTCGTCTTTTTGATCCCTGGGGAGGTTATGACATGATTGGATTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcacgttctagttgattactatattcttctgtttgtgtaaatttatggcatagGTTGCACGTGGGAGCAAAGACACTGGAGAATCTATTCCCATGCTTTTGAGAATTCCACGGCTTTCTGATCCATGGGGTGGTTACAACATGATCGGTTTTG
agttgat putative branch site (score: 5)
tttgtgtaaatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacatagcgagaacgaagaaggtcgatgataggttaactaacctcaatcacgttctagttgattactatattcttctgtttgtgtaaatttatggcatagGTTGCACGTGGGAGCAAAGACACTGGAGAATCTATTCCCATGCTTTTGAGAATTCCACGGCTTTCTGATCCATGGGGTGGTTACAACATGATCGGTTTTG
- - - - - - -cgaagaa
- - - - - - - - - - - - - - - - - -aactaac
- - - - - - - - - - - - - - - - - - - - - - caatcac