Sequence
atgc intronic sequence ATGC exonic sequencegtataaaccaagcttttggtcttcacttaaaatttgcaccctttgtgttctgcttgaataattctggtttctctgctaaatgattagGTTGCTAATTGGTTCATAAACGCGAGAGTTCGTCTGTGGAAACCGATGATCGAAGAAATGTATAAAGAAGAGTTTGGTGATGAATCTGAGTTACTAATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G19700.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G19700.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g47740.2 (Oryza sativa), 3'ss of exon 5
--gtataaaccaagcttttggtcttcacttaaaatttgcaccctttgtgttctgcttgaataattctggttt-ctctgctaaatgat--------------tagGTTGCTAATTGGTTCATAAACGCGAGAGTTCGTCTGTGGAAACCGATGATCGAAGAAATGTATAAAGAAGAGTTTGGTGA--TGAATCTGAGTTACTAATCT
| |||| | |||| | | || || ||||||| || | | ||| ||| | |||| || || | || ||| || | |||||||||||||| || | || || ||||||||||||||||||||||| ||||||||||||||| |||| || | |||| | | ||
gtttgtaaattac-ctttctttttgca---gaactttgcactctgcatcaattcattggatagaattagtttgctgaactcaccaatattcttctttgtcctagATTTCAAATTGGTTCATAAATGCCCGTGTCCGCCTGTGGAAACCGATGATCGAAGACATGTATAAAGAAGAGATTGGGGAGGCGGATCTCGACT-CGAACT-
upper sequence: AT1G19700.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g43950.1 (Oryza sativa), 3'ss of exon 5
--------------------gtataaaccaagcttttggtcttcacttaaaatttgcaccctttgt--------------gttctgcttgaataattc--tggtttctctgctaaatgatt------------agGTTGCTAATTGGTTCATAAACGCGAGAGTTCGTCTGTGGAAACCGATGATCGAAGAAATGTATAAAGAAGAGTTTGGTGATG-AATCTGAGTTACTAATCT
| | || | ||| || || || | ||| || || | || | ||| || | ||| || ||||| ||| || || || | |||||||||||||| || | || || || |||||||| ||||| ||||| ||||| ||||||||| |||||||| | || | ||
gtaaatattgtttatcttttttgtgcactggaccattgatccacatttgatgttttaacttcttatcctagaagcattttgtgtttcttcaagagttcaacatgttgactgcttcatgcttctcctgttctccagATTTCGAATTGGTTCATAAATGCCCGTGTCCGCCTTTGGAAACCAATGATTGAAGACATGTACAAAGAAGAGATTGGTGATTTAGAGCAAGACTCCAACT-
upper sequence: AT1G19700.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G011588_T03 (Zea mays), 3'ss of exon 5
-gtataaaccaagcttttggtctt-cacttaaaatttgcaccctttgtgttctgcttgaa----taattctggtttctctgctaaatgatt-------agGTTGCTAATTGGTTCATAAACGCGAGAGTTCGTCTGTGGAAACCGATGATCGAAGAAATGTATAAAGAAGAGTTTGGTGA--TGAATCTGAGTTACTAATCT
| | | | | ||| | | | | | |||| | | | | | | ||| || || | ||| | | || || || | || |||||||| || || | || || |||||||| || ||||||||||| ||||| ||||||||| ||||||| | | || | | | |
cctgtgatctgatgacttgctgtcatattagtagtttgtattccgtatcaaataatggaaaccatatttactgaaactcacatgcgtccttctattctagATTTCAAACTGGTTCATCAATGCCCGTGTCCGGCTGTGGAAGCCAATGATCGAAGACATGTACAAAGAAGAGATTGGTGAAGCGGAGCTAGACTCCAACT-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcaccctttgtgttctgcttgaataattctggtttctctgctaaatgattagGTTGCTAATTGGTTCATAAACGCGAGAGTTCGTCTGTGGAAACCGATGATCGAAGAAATGTATAAAGAAGAGTTTGGTGATGAATCTGAGTTACTAATCT
tgctaaa putative branch site (score: 2)
ttgaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaaccaagcttttggtcttcacttaaaatttgcaccctttgtgttctgcttgaataattctggtttctctgctaaatgattagGTTGCTAATTGGTTCATAAACGCGAGAGTTCGTCTGTGGAAACCGATGATCGAAGAAATGTATAAAGAAGAGTTTGGTGATGAATCTGAGTTACTAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG