Sequence
atgc intronic sequence ATGC exonic sequence...attctcttgatttattgaccagaatttgcatttgcatgggcgatagtggagctattaaacttgtaagatttattgattgaattttctgtttctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G78920.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 6
attctcttgatttattgaccagaatttgcatttgcatgggcgat-agtggagctattaaacttgtaagatttattgattgaattttctgtt--tctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC
| || || || || | | | || | | | || || ||| |||| || | | || |||| || | ||||| || | || | ||| |||||||| ||||| ||||||||||||||||| || ||||| ||| | |||||||||||||||||||||||||| || || | |||||||| || ||
--tttcctggttgataacactggttatggttatatgtttgcaattagttcttttattcaaatgg-aatatttcttttgtcaatttcacatttatttcctgtagTGCCTCTTCTCCTTGTGGGATATGGTTTTGGTGCGTCTTTTGTCGCCCTTTTTGCTCAGTTGGGTGGTGGAATATACACCAAAGCTGCTGATGTCGGAGC
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------attctcttgatttattgacc--agaatttgcatttgcatgggcgatagtggagctattaaacttgtaagatttattgattgaattttctgtttctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC
|| ||| ||||||| || ||||| | ||| ||| | | | || | | ||||| | | | | ||| | ||| |||||||| ||||| ||||||||||||||||| || ||||||||| | |||||||||||||||||||||||||| || || | ||||||||||| ||
gtaagtttcttgtacacaatacacctgaaaacacactagattacaatccaacttgtccaccaattatctacttattttattgtttttgcaaattgcaataccattttgttatgtgaaaggaacattattctg----ctgctgattcatatgttttttttgtgtgtagTGCCTCTTCTCCTTGTGGGATATGGTTTTGGTGCCTCTTTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATACACGAAAGCTGCTGATGTTGGAGC
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 6
------attctcttgatttattgaccagaatttgcatttgcatgggcgatagtggagctattaaacttgtaagatttattgattgaattttctgtttctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC
|| | | |||| ||| || | | || | | | || | || |||| | || ||| || || || ||||| ||| |||| ||||||||||| || |||||||| |||||||| || |||||||| |||||||||||||||||||||||||||| || |||| |||||||||||| ||
tatgacatgatttaaattt-ttgtccgttctgt-cacctattctctctctccctct-ctctctaatttgtca--ttgattttttaaaattcttgttttcctt-cagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCTCAGTTGGGTGGTGGAATATACACAAAGGCAGCTGATGTTGGAGC
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 6
attctcttgatttattgaccagaatttgcatttgca---tgggcgatagtggagctattaaacttgtaagatttattgattgaattttctgtttctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC
| | | ||| ||||| || | | || | || | | | ||| ||| |||| |||| || || | |||| ||||||||||| || |||||||| |||||||| || |||||||| ||||||| |||||||||||||||||||| || |||| ||||||||||| ||
--tttgaccgtgacatgattttaatttttgttcattctctcacctattctctctctctctcaaattggcgatcgattt-ttgagcattcttgttttccttcagTGCCTCTTCTTCTAGTTGGATATGGATTTGGTGCCTCCTTTGTTGCACTATTTGCCCAGTTGGGTGGTGGAATATACACAAAGGCCGCTGATGTTGGAGC
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 6
attctcttgatttattgaccagaatttgcatttgcatgggcgatagtggagct--attaaacttgtaagatttattgattgaattttctgt--ttctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC
| || | | | | | | ||||| | || | || | | ||||| | || || | || ||||| || ||| |||| | |||| |||||||||||||| |||||||| ||||| ||||| ||||||||| | ||||||||||||||||||||||||||||| || | ||| |||||||| ||
----tttttacatctcttttacacctaccattttcttgaattagcatgcacatgtattaatgtggtgtaatctgtttattgacttcaatgtacttctttcccagTGCCTCTTCTTCTTGTGGGATATGGATTTGGAGCTTCATTTGTTGCCCTTTTTGCTCAGTTGGGTGGTGGAATATATACAAAAGCAGCAGATGTTGGAGC
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S105_42V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------attctcttgatttat-tgaccagaatttgcatttgcatgggcga-------tagtggagct-------attaaacttgtaagatttat------tgattgaattttctgtttctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC
| || | ||| | | | | || ||| || | || | ||| | || || | | | | ||||| | | ||| | | | | | || |||| ||| | || || || || |||||||||||||||||||||||||| | ||||| || | || || || |||||||| || | || || || || ||
gtgaggggccttacttttctttcctattttgtgcgcctaaaacttgttttgagcttggtggattgacctagaacaacttctcatgatcacattcagaggatttgtatgtgttcattaatgatgttttccatgttgcagTGCCTTTGCTGCTGGTTGGCTATGGTTTTGGTGCTTCGTTTGTTGCGCTCTTTGCACAACTAGGAGGGGGGATATATACAAAAGCTGCAGACGTAGGTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggagctattaaacttgtaagatttattgattgaattttctgtttctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC
tattgat putative branch site (score: 3)
ttttctgtttctctta putative PPT
tattaaacttgtaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attctcttgatttattgaccagaatttgcatttgcatgggcgatagtggagctattaaacttgtaagatttattgattgaattttctgtttctcttacagTACCTCTTCTTCTTGTCGGATATGGTTTTGGTGCTTCGTTTGTTGCCTTATTTGCTCAGTTGGGTGGTGGAATATATACTAAGGGAGCTGATGTTGGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - -accagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -attaaac