Sequence
atgc intronic sequence ATGC exonic sequencegtatgtagtttatttatgagaccattgttgtatcaaaggaacatagattcacattaaatttcttgttattacgcagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06160.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G06160.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
--------------gtatgtagtttatttatgagaccattgttgtatcaaa--ggaacatagattcacattaaattt-------cttgt-tattacgcagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC
| | | || |||||| | | || |||| | ||| || || || | ||| | || ||||| || || || ||||||||||| ||| ||||||||||||| ||||||||| |||| | ||||| || |||||||| || || || || ||||| ||||
accagaaaatcaaggcacctttttcttttatgcttagtaagctctagcaaatttgttttctgatgcatttttaactgttatggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
upper sequence: AT5G06160.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 10
-------------------------gtatgtagtttattta-tgagaccattgttgtatcaaaggaacatagattcacattaaatttcttgttat--tacgcagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC
||| | | || | || | || || || ||| | | | ||| |||||||| | ||| | ||||| ||||| || |||||||| |||||||| || |||||||| | ||||||| || ||||||||||||||||||| || ||||| || ||||| || |
ataaatctgttgacccattaaaagggtacggacttgttatagtaggattctttatggctcacaatatt-tggat---cattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
upper sequence: AT5G06160.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G13290.1 (Glycine max), 3'ss of exon 10
--------------------------gtatgtagtttatttatgagaccattgttgtatcaaaggaacatagattcacattaaatttcttgttat-tacg-cagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC
||| | | || | ||| || || || ||| || | | ||| |||||||| | ||| || ||||| ||||| || |||||||| |||||||| || |||||||| | ||||||| || ||||||||||||||||||| || ||||| || ||||| || |
gataaatctgttaactgattaaaagggtagggacttgttgtataggattctttatggctcacagtatttt-gat---cattaaataatataatatgtatttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC
upper sequence: AT5G06160.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S218_51V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------------gtatgtagtttattta---tgagaccattgttgtatcaaaggaacatag-attcacattaaatttcttgttattacgcagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC
| || | | || | | | |||||| | | | | | | | | | ||| | || || | |||||||||||||| |||||||| || || |||||||||||||| || |||||||||| |||| || || |||||| |||| || || |||||||||||
taagacgcttggccgtagaaatgaatttcggttctgcagtgtaggaccatctcttttttctcgcagctttgcacctggattga--cgagtgataattttcagGAGTTTAAATGTGAGATATGCGGCAATTATAGCTATTGGGGTCGACGGGCTTTTGAACGACACTTCAAGGAATGGAGACATCAGCATGGAATGCGTTGTT
upper sequence: AT5G06160.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ22878 (Selaginella moellendorffii), 3'ss of exon 9
gtatgtagtttatttatgagaccattgttgtatcaaaggaacatagattcacattaaatttcttgttattacgcagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC
|| | || | | | | ||| | || | || || ||||||||| ||||||||||||||||| |||| ||||| ||||| ||||||| || || |||| || ||||||||| | || || ||||| ||||| |||
-------------gtaaaaagttatgctccttcttttg-----caagccttcatctcctctcct-ttgttttgcagGAGTTCAAATGCGAGATATGTGGAAACTCCAGCTACTGGGGGCGAAGGGCCTTCGAACGACACTTCAAAGAATGGAGGCATCAGCACGGCATGCGCTGCT
upper sequence: AT5G06160.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ30765 (Selaginella moellendorffii), 3'ss of exon 9
gtatgtagtttatttatgagaccattgttgtatcaaaggaacatagattcacattaaatttcttgttattacgcagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC
|| | ||| | | | | ||| | || | || || ||||||||| ||||||||||||||||| |||| |||||| ||||| ||||||| || || |||| || ||||||||| | || || ||||| ||||| |||
-------------gtaaaaagttattctccttcttttg-----ctggccgtcatctcctctcct-ttgttttgcagGAGTTCAAATGCGAGATATGTGGAAACTCTAGCTACTGGGGGCGAAGGGCCTTCGAACGACACTTCAAAGAATGGAGGCATCAGCACGGCATGCGCTGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccattgttgtatcaaaggaacatagattcacattaaatttcttgttattacgcagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC
tttcttgtt CT-rich tract
acattaaatttcttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtagtttatttatgagaccattgttgtatcaaaggaacatagattcacattaaatttcttgttattacgcagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA