Sequence
atgc intronic sequence ATGC exonic sequencegtgagcatttatttctctttgctttccataaactttgaattgtatatggaaagataataactttttctttatattttactcagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28610.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g21240.1 (Oryza sativa), 3'ss of exon 3
-------------------gtgagcatttatttctctttgctttccataaactttgaattgtatatggaaaga---taataactttttctttatatttta--------ctcagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG
| || | | | ||| || ||| || |||| ||| | | | ||||| ||||| ||| || | |||| ||||||||| ||||| || || ||| ||||||||||||| || ||||| || ||||||||||| || ||| | |||
gtatgtcctccgtgtcgtaaataccactcaagtggttttctcttatatatac---gaatcctattctggcatagtctaatagttttttttttttaaaaaaaaaaaaccttcagAAGCTACTCCAAAAGGTGTGCTCAAGCTTATGAAAGTTGATGGTTTGACAATCTATCATGTTAAGAGTCATCTGCAG
upper sequence: AT4G28610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G006477_T02 (Zea mays), 3'ss of exon 3
-------------gtgagcatttatttctctttgcttt---ccataaactttgaattgtat-atggaaag---ataataactt-tttctttatattt-tactcagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG-----------------------
| |||||| | ||| || ||| | || || || || | | | | || | | || |||| || |||| |||||||||||| || || || ||| ||||||||||||| || ||||||||||||||||| |||||||| | |||
gtatgtctgccctattggcatttcccctcaaatagtttaagttatgaaccctacatcacatcatctaatgcatgtgtttatttatcttttcttattcctattcagAAGCTACTCCTAAGGGTGTGCTAAAGCTTATGAAAGTTGATGGTTTGACTATATATCATGTCAAAAGCCACCTGCAGGTTTGCTGTTTAGCTTTCTAAGT
upper sequence: AT4G28610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G006477_T01 (Zea mays), 3'ss of exon 3
-------------gtgagcatttatttctctttgcttt---ccataaactttgaattgtat-atggaaag---ataataactt-tttctttatattt-tactcagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG
| |||||| | ||| || ||| | || || || || | | | | || | | || |||| || |||| |||||||||||| || || || ||| ||||||||||||| || ||||||||||||||||| |||||||| | |||
gtatgtctgccctattggcatttcccctcaaatagtttaagttatgaaccctacatcacatcatctaatgcatgtgtttatttatcttttcttattcctattcagAAGCTACTCCTAAGGGTGTGCTAAAGCTTATGAAAGTTGATGGTTTGACTATATATCATGTCAAAAGCCACCTGCAG
upper sequence: AT4G28610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G32350.1 (Glycine max), 3'ss of exon 4
--gtgagcatttatttctctttgctttccataaactttgaattgtatatggaaagataataactttttctt-tatattttactcagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG
|| || | | ||||||| | || ||| | | || | | | | |||| | | | ||| |||||||||| |||||||| || |||||| | |||||||||||||| || |||||||| |||||||||||||| |||||
gtatgtctatctttctctcttttcaaagcaaggccttagtttcttaaacttctgtctccttatttttccccattttctttttacagGAGCTACCCCTAAAGGTGTGCTGAAGCTCATGAAAGTTGAAGGATTAACTATATACCATGTTAAAAGCCACCTACAG
upper sequence: AT4G28610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G04540.1 (Glycine max), 3'ss of exon 4
--gtgagcatttatttctctttgctttccataaactttgaattgtatatggaaa-----gataataa--------ctttttctttatattttactcagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG
| | ||| | ||| || | ||| | | || | | || | | || |||||||| | | ||| ||| ||||||||| || || || |||||| | |||||||||||||| || |||||||||||||||||||||||||| |||
gtgcggtcatctttttttcctctgtttgttaagtccttagccttagtttgctagcctctgtccttattttcccccctttttctgtcttctttctacagAAGCTACTCCAAAGGGTGTGCTGAAGCTCATGAAAGTTGAAGGATTAACTATATATCATGTTAAAAGCCATTTGCAG
upper sequence: AT4G28610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G18800.1 (Glycine max), 3'ss of exon 1
--gtgagcatttatttctctttgctt------tccataaactttgaattgta---tatggaaagataataac---tttttctttatattttactcagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG
| || | ||||||| || || ||| || ||| | | || | || || | | ||||||| | | ||| ||| ||||||||| || || || |||||| | |||||||||||||| || |||||||||||||||||||||||||| |||
gtacggtgatctttttctctctgtttgttaagtccttagccttagtttgctaacctttgtcctcattttcccctgtttttctgtctgctttctacagAAGCTACTCCAAAGGGCGTGCTGAAGCTCATGAAAGTTGAAGGATTAACTATATATCATGTTAAAAGCCATTTGCAG
upper sequence: AT4G28610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G35080.1 (Glycine max), 3'ss of exon 4
--gtgagcatttatttctctttgctttccataaactttgaattgtatatggaaagataataactttttctttatattttact-cagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG
|| || | | ||||||| | | || ||| | | || | | | | |||| | ||| || | |||||||||| |||||||| || |||||| | ||||||||||| || || |||||||| |||||||||||||| |||||
gtatgtctatctttctctcttttcaatgcaaggccttagtttcttaaacttctgcctccttatttttccccattatctttttacagGAGCTACCCCTAAAGGTGTGCTGAAGCTCATGAAAGTTGATGGATTAACTATATACCATGTTAAAAGCCACCTACAG
upper sequence: AT4G28610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g04120.t01 (Vitis vinifera), 3'ss of exon 3
gtgagcatttatttctctttgctttccataaactttgaattgtatatgga------------aagataataactttttct-ttatattttactcagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG
| | || ||| | || || | | | || || ||| |||| ||| | || |||| | || |||| || |||||||||||||||| || ||||||||| | |||||||| |||||||| || || |||||||| |||||||| || |||
----gtgtgtacccctcctagccttactttactgtttaaccttatttggacaatacaattataaggtcctagctttaattgttttattataaacagGAGCTACTCCTAAGGGTGTACTGAAGCTCATGAAAGTGGAAGGCTTAACCATCTATCATGTAAAAAGCCACTTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaactttgaattgtatatggaaagataataactttttctttatattttactcagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG
taataac putative branch site (score: 1)
ctttttctttatattt CT-rich tract
tatatggaaagataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcatttatttctctttgctttccataaactttgaattgtatatggaaagataataactttttctttatattttactcagGAGCTACTCCTAAAGGGGTACTGAAGATTATGAAAGTTGAAGGCTTGACTATATATCATGTTAAAAGCCATTTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG