Sequence
atgc intronic sequence ATGC exonic sequence...ccactaaggattgtaaagatatatgcttgtagaaaaccaaatagctcttcgtagttccgacatgacttggaatcagattttataatatactgtcttgcagCACAGTGCAAACGAGTTTGAGAGACTGTTAAAGGAAATGTGTGCTGATGAGGATGGAGATTTACTAATAGAATCAGCTGTGAAGAATGTTCCAAAAGTAT
Basic information
| species | Arabidopsis thaliana |
| transcript | AT1G61850.1 |
| intron # | 9 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 8
ccactaaggattgtaaagatatatgcttgtagaaaaccaaatagctcttcgtagttccgacatgacttg----gaatcagattttataatatactgtcttgcagCACAGTGCAAACGAGTTTGAGAGACTGTTAAAGGAAATGTGTGCTGATGAGGATGGAGATTTACTAATAGAATCAGCTGTGAAGAATGTTCCAAAAGTAT
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--atgatgcattattgcattcttttctctgagctatttagcta--ttttgggtgtttgaattttctctgccctaaatggagtattatgacttattgtcttgcagCATAGTGCAGAACAGTTTGAAAGGCTATTGAAGGAAATGTGTGCTGATGAAGATGGAGATCTAATGATAGATTCTGCTGTGAAAAATGTGCCCAAAGTTT
upper sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G01850.1 (Glycine max), 3'ss of exon 9
ccactaaggattgtaaagatatatgct-tgtagaaaaccaaa---tagctcttcgtagttccgacatgacttggaatcagattttataatatactgtcttgcagCACAGTGCAAACGAGTTTGAGAGACTGTTAAAGGAAATGTGTGCTGATGAGGATGGAGATTTACTAATAGAATCAGCTGTGAAGAATGTTCCAAAAGTAT
|| | | | | | ||| ||| | | || | | | | ||| | || | | || | || | || || | |||| | || |||||||||||| |||||| | |||| || || || || |||||||||||||||||||| ||||||||| || | ||||| || |||||||| ||||| || ||||| |
gcattcttttctctga-gctattagctattttgacagcgataatctaggtatttgaattttc--tctgcactaaaaggag-tattatgacttattgtcttgcagCATAGTGCAGAACAGTTCGAAAGGCTATTGAAGGAAATGTGTGCTGATGAAGATGGAGATCTAATGATAGATTCTGCTGTGAAAAATGTGCCCAAAGTTT
upper sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------------------ccactaaggattgtaaagata------tatgcttgtagaaaaccaaatagc-tcttcgtagttc--cgacatgacttggaatcagattttataatatactgtcttgcagCACAGTGCAAACGAGTTTGAGAGACTGTTAAAGGAAATGTGTGCTGATGAGGATGGAGATTTACTAATAGAATCAGCTGTGAAGAATGTTCCAAAAGTAT
| | || | || | | | ||| ||| | | | | | || ||| | | ||| ||| ||| |||| ||| |||||||||||||||| | |||||||||| ||||||||||||||||||| |||||||| ||||| | ||||||| ||||| ||||| || ||||||| || |
gtatgaaatattctttttctctttatattccttcagagatttcttcatcccaatcaaatacacccaacttcccccctttttctttcagaggagtggggggagtgaatgaaatttgttattatggcctaaaatgagacactatcatattctgccttgcagCACAGTGCAGATCAGTTTGAGAGGTTGTTAAAGGAAATGTGTGCAGATGAGGAAGGAGACCTGTTAATAGAGTCAGCAGTGAAAAACATTCCAAAGGTTT
upper sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S69_157V6.1 (Physcomitrella patens), 3'ss of exon 9
ccactaaggattgtaaagatatatgcttgtagaaaaccaaatagctcttcgtagttccgacatgacttggaatca-------gattttataatatactgtcttgcagCACAGTGCAAACGAGTTTGAGAGACTGTTAAAGGAAATGTGTGCTGATGAGGATGGAGATTTACTAATAGAATCAGCTGTGAAGAATGTTCCAAAAGTAT
|| |||| || | | || | | ||||||| |||| || || || || | || | | || ||||||| ||| | | |||||| || | || || ||||| || |||||||| || ||||||||||| |||||||| |||||| ||||||||||| |
---cttctgatttctgcttcgtaagtt----gagttcattgtggctcttcaacgttcaaacgtggtcgagagacattgatggggcattcttgtgggcttcaaaacagCACAATGCGGAGCAATTTGAGCATTTGCTGAAAGAGATGTGCGCAGATGAGGAGGGGGATTTACTAATTGAATCAGCAGTGAAGGGCGTTCCAAAAGTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcgtagttccgacatgacttggaatcagattttataatatactgtcttgcagCACAGTGCAAACGAGTTTGAGAGACTGTTAAAGGAAATGTGTGCTGATGAGGATGGAGATTTACTAATAGAATCAGCTGTGAAGAATGTTCCAAAAGTAT
ctgtctt CT-rich tract
aatcagattttataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccactaaggattgtaaagatatatgcttgtagaaaaccaaatagctcttcgtagttccgacatgacttggaatcagattttataatatactgtcttgcagCACAGTGCAAACGAGTTTGAGAGACTGTTAAAGGAAATGTGTGCTGATGAGGATGGAGATTTACTAATAGAATCAGCTGTGAAGAATGTTCCAAAAGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
ccactaa
- - - - - - - - - - - - - - - - - aaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaga
