Sequence
atgc intronic sequence ATGC exonic sequence...gaaaaaaaaaaaatctggagcttgtttatgaatcatgtattttgatgaaacagctgatgctatgctacatgctgatacaatttgcattttgatgaaacagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G28850.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 6
gaaaaaaaaaaaatctggagcttgtttatgaatcatgtattttgatgaaac--agctgatgctatgctacatgctgatacaatttgcattttgatgaaa----cagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT
|| || | | | |||||| |||| | | ||| | ||| ||||| | || ||| || | |||||| |||| || ||||| | |||||||| ||||||| ||||||||||||||| ||||||| | || | || ||||| ||||| ||||| ||||||| ||| |
-----aactcaactatctattttgttttaagatcagatttgctgaatgttttgaactgttgctaatgtttgctgtgtcaca-ttcatttcttgatgttttcttcagCGGAGACTGTAATATACAGAATCTTTTACTCCATAAATAGATCTGGGAATGGTCATCTGACTCTGAGAGAGCTCAAACGTGGAAATTTAATTGCTGCACT
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 6
---gaaaaaaaaaaaatctggagcttgtttatgaatcatgtattttgatgaaacagctgatgctatgctacatgctgatacaatttgcatttt-gatgaaacagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT
| | | || | | ||||||| | | ||| | | || || ||| | | | | || ||||| ||| ||| ||||||||||||||| |||||||||| ||||||||| |||||||| || |||||||| |||| | |||||||| ||||| |||||| |||||||||| ||
gttgggcataggctggtcatca--tagtttatggtgtaatgctcttgttttgtcttttg-tgtggtgcaatgttcata-actatttgtttttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGTCGTCTTACCCTGAGGGAGCTGAAACGTGGAAACATAATTGATGCAAT
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 6
----gaaaaaaaaaaaatctggagcttgtttatgaatcatgtattttgatgaaacagctgatgctatgctacatgctgatacaatttgcattttgatgaaacagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT
| | | | ||| | | | ||| || | | || ||| ||| | ||| | ||| || ||| ||||||||||||||| |||||||||| ||||||||| |||||||| || ||||| || |||| | ||||||||||| || |||||| |||||||||| ||
cttcatatatttgagtgttgggaaaatcagttaaaggattgttttgtctttttgtgtgtggtgcaatgtt-cataactgtttgtttt---ttccaatggcccagCTGAAACTGTCATATACAGAATATATTACTACATTAATAGATCAGGAAATGGCCGTCTTACCCTGAGGGAGCTTAAGCGTGGAAACATAATTGATGCAAT
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 6
---gaaaaaaaaaaaatctggagcttgtttatgaatcatgtattttgatgaaacagctgatgctatgctacatgctgatacaatttgcatttt-gatgaaacagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT
| | |||| ||| || | || ||| | || ||| | || || |||||| |||| ||| ||||||||||||| | |||||||| | ||| ||||| ||||||||||| |||||||| | || | |||||||| || || |||||| |||||||||| ||
tgctagttttctttcaactggtctttggtttctggtgtaatacttttttttttttttgcattgagtgcaatattct----taatttgttttttcaatgtcccagCTGAAACTGTAATATACAGAATCTATTATTACATTAATAGATCTGGAAATGGTCGTCTCACCCTGAGGGAGCTGAAGCGTGGAAACATAATTGATGCAAT
upper sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------gaaaaaaaaaaaatctggagcttgtttatgaat-----catgt----attttga--tgaaacagctgatgct-atgctacatgctgatacaatttgc-attttgatgaaacagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT
|| ||| | | | | ||| ||||| |||| ||||| | | | | || || || || | || | | ||| | ||| || | ||||||||||||| | |||||||||||| ||| | |||||| |||||| |||||||| | | |||| ||| | |||||| | ||||||||| |||| |
gtacgacttcgttacaaattctgcacatgatctatgcactgatcctgtaaagacttcaatggtatttttgaatgctagcatgattagattttcaacttgagtaatgcatcctgattctttgtactccaatgaaatgctgtgttggtgga-cagCTGAAACTGTGATCTACAGAATATTCTACCATGTAAATAAATCTGGGAATGGTCGGCTACAACTTAGAGAGTTAAAACGGAGTAACTTAATTACTGCTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaacagctgatgctatgctacatgctgatacaatttgcattttgatgaaacagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT
atacaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaaaaaaaaaaatctggagcttgtttatgaatcatgtattttgatgaaacagctgatgctatgctacatgctgatacaatttgcattttgatgaaacagCTGAAACTGTCACCTACAGAATATTTTACTACATAAATAGATCTGGCAATGGTCGAATTACATTTAGGGAGCTTAAACGGGGAAACTTAATTGATGCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT