Sequence
atgc intronic sequence ATGC exonic sequencegtgagaattaatgaattgattttctggagtaatgattaggattcgttttatttttggtttctgattactcgtttgttattagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13470.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
------gtgagaattaatgaattgattttctggagtaatgattaggattcgttttatttttggttt----ctgattactcgtttgt---tattagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA
| | || || | || || | | | || | | || | ||| ||| || |||| | ||| | | | ||||||| || |||||||| || ||||||||||| || ||||| |||||||| || || ||||||||| | |||||||||||||| ||||| || ||||| |
gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgaccaggcactcattagttatttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 2
gtgagaattaa--tgaattgatttt--ctggagtaatgattaggattcgt----tttatttttggtttctgattactcgtttgt-tattagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA
||||| || | | | |||| || | | ||| || || | | | || || || ||| | || ||| | | ||| ||| || || ||||| || || || ||||| ||||| ||||| |||||||| | |||||||| |||||||||||||||||||| || | |||||| |
gtgagttgtacattctaataatttctactagcatgatg-ctatcatctataacatcaacttctgagttgtgacttctattttctatgacagAATGGAGTCAATAAGCTTGCTGATCTCGTTGGAGTCACCCTTGGTCCAAAAGGACGGAATGTTGTCCTTGAGAGCAAGTATGGATCACCTAAAATTGTCA
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G133698_T02 (Zea mays), 3'ss of exon 2
gtgagaattaatgaattgatt--ttctggagtaatgattaggattcgttttatttttggtttctgattactcgtttgt-------tattagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA
||||| | | || ||| || || || |||| | | | | | || ||| | || | | ||||||| || || ||||| || ||||| || || || ||||| |||||||| || || ||||||||| | |||||||||||||| || || | ||||||||
gtgagctccacagtttttatttattatgatataccgatttgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 1
gtgagaattaatgaat-tgattttctg-gagtaatgattagga----ttcgttttatttttggtttctga-ttactcgtttgttat-tagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA
|| | ||| | | ||| || || ||||| || |||||| | | |||| ||| || | ||| | ||| ||||| |||||||||||||| || ||||| ||||| ||||| || || || |||||||||||||| |||||||||||||| || || | ||| ||||
gtataatataacactcctcgctcgctgtgactagtgattgcgaaacgcgcgttttgagtgtcgtttttgagtttttttcgcgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGAAATGTTGTTCTCGAGAGCAAGTATGGCTCGCCGAAAATCGTTA
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 1
gtgagaattaatgaattgattttctggagtaatgattaggattcgttttatttttggtttctg-attactcgtttgttat-tagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA
| | | | | | || ||| |||| | || ||| | | | | |||| | ||| ||||| |||||||||||||| || ||||| ||||| ||||| || || || || ||||||||||| || |||||||| || || || | ||| ||||
------------gtacgtgctgtatatcgctgtggctagtgatcgtgaaacgcgtgttttgagtgtcgtttttgtgttttgcagAGCGGTGTGAACAAGCTCGCGGATCTGGTTGGGGTCACGCTTGGTCCCAAGGGAAGGAATGTTGTTCTCGAAAGCAAGTACGGCTCGCCGAAAATCGTTA
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------gtgagaattaatgaattgattttctggagtaatgattaggattcgttttatttttggtttctg-attactcgtttg---ttattagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA
|| | | | |||||| | | | || || || | | || || || || || || | ||||||| || || || || || || || || || || || ||||| |||||||| || |||||||| || |||||||||||||| ||||||| ||||||||
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaacattttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtaatgattaggattcgttttatttttggtttctgattactcgtttgttattagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA
ttctgat putative branch site (score: 3)
ctcgttt putative PPT
attcgttttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaattaatgaattgattttctggagtaatgattaggattcgttttatttttggtttctgattactcgtttgttattagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG