Sequence
atgc intronic sequence ATGC exonic sequence...gttcaaatatatgatttatttctatgcacaaacgttagttgcatattgttaaaccaataagacatagcactcactcatggtatacttttcctttacttagGACATTGAAATCGGACAACGAATGATTACAATATCGACTGTAGGTGTTCCAAACACAATCAAGAAGCTTGCATCTCATAAGCTTCAGTCGACCTTAGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39670.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G168412_T01 (Zea mays), 3'ss of exon 5
-------------------------gttcaaatatatgatttatttctatgcacaaacgttagttgcatattgttaaaccaataagacatagcactcactcatggtatacttttcctttacttagGACATTGAAATCGGACAACGAATGATTACAATATCGACTGTAGGTGTTCCAAACACAATCAAGAAGCTTGCATCTCATAAGCTTCAGTCGACCTTAGCTG
||| | ||| || |||| || | || |||| || | ||||| ||| | | || || | |||| | | |||| | |||| || ||| | ||||| |||||||| || || ||||||||||| ||||| || | ||| |||||||| ||||||||||| || | || |
gtctgttgacaagtaactaggctacattcctctcatcctgttaatttgatgcgacaatttaccatgaatatctttccat--ataagctataactttaacaagtg-cgtggatttcatgctgtcagGAACTAAAAATTGGGCAAAGGATGATGACAATATCTACAGTTGGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAG
upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G095663_T01 (Zea mays), 3'ss of exon 1
--------------------gttcaaatatatgatttatttctatgcacaaacgttagttgcatattgttaaaccaataagacatagcactcactcatggtatacttttcctttacttagGACATTGAAATCGGACAACGAATGATTACAATATCGACTGTAGGTGTTCCAAACACAATCAAGAAGCTTGCATCTCATAAGCTTCAGTCGACCTTAGCTG
| | || ||| |||| |||| || | | ||| | | ||||| ||| | | || || | | |||| | | |||| | |||| || ||| | ||||| |||||||| || || ||||||||||| ||||| || | ||| |||||||| ||||||||||| || | || |
gtgtttgtaactaggctacattcctctcatcctattaatttg-atgcgataatttaccataagtatctctccat--ataagctataactttaacaagtg-tgtggatttcatgctgtcagGAACTAAAAATTGGGCAAAGGATGATGACAATATCTACGGTTGGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAG
upper sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G395039_T01 (Zea mays), 3'ss of exon 4
-------------------------gttcaaatatatgatttatttctatgcacaaacgttagttgcatattgttaaaccaataagacatagcactcactcatggtatacttttcctttacttagGACATTGAAATCGGACAACGAATGATTACAATATCGACTGTAGGTGTTCCAAACACAATCAAGAAGCTTGCATCTCATAAGCTTCAGTCGACCTTAGCTG
||| | ||| || |||| || | || ||| | | ||||| || | | || || | |||| | | |||| | |||| |||||| | ||||| |||||||| || || |||||||||| ||||| || | ||| |||||||| ||||||||||| || | || |
gtctgttgacaagtaactaggctacattcctctcatcctgttaatttgatgcgacaatttaccatgagtatctctccat--ataagctatgactttaacaagtg-cgtggatttcatgctgtcagGAACTAAAAATTGGACAAAGGATGATGACAATATCTACAGTTAGTGTTCCAAATACAATAAAAATGCTAGCATCTCACAAGCTTCAGTCAACGCTGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttaaaccaataagacatagcactcactcatggtatacttttcctttacttagGACATTGAAATCGGACAACGAATGATTACAATATCGACTGTAGGTGTTCCAAACACAATCAAGAAGCTTGCATCTCATAAGCTTCAGTCGACCTTAGCTG
cactcac putative branch site (score: 2)
tacttttcctttactt putative PPT
tatactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcaaatatatgatttatttctatgcacaaacgttagttgcatattgttaaaccaataagacatagcactcactcatggtatacttttcctttacttagGACATTGAAATCGGACAACGAATGATTACAATATCGACTGTAGGTGTTCCAAACACAATCAAGAAGCTTGCATCTCATAAGCTTCAGTCGACCTTAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC