Sequence
atgc intronic sequence ATGC exonic sequence...tttgtgaaatttgctttgaaaacgcttttgatctacatcagtcaggatcgtaattgcagataatcatttttgattcctaagttgatttttaatgtattagGTGGCATCAAAAACCGAGTCAAACAAAAATGCAGGGAATGCTATCCTATACGAATGCGTTCAAACGATAATGAGCATCGAAGAAAATGGTGGCCTACGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G60070.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 5
--tttgtgaaatttgctttgaaaacgcttttgatctacatcagtcaggatcgtaattgcagataatcatttttgattcctaagttgatttttaatgtattagGTGGCATCAAAAACCGAGTCAAACAAAAATGCAGGGAATGCTATCCTATACGAATGCGTTCAAACGATAATGAGCATCGAAGAAAATGGTGGCCTACGAG
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tatgtgagtaaatgaattttaatctactattgcttattattggtggtcatctcttcggaaattcaagactgataatttttacacttgctgcc--tggtttagGTGGCTACAAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG
upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 4
-tttgtgaa-atttgctttgaaaacgcttttgatctacatcagtcaggatcgtaattgcagataatcatttttgattcctaagttgatttttaatgtattagGTGGCATCAAAAACCGAGTCAAACAAAAATGCAGGGAATGCTATCCTATACGAATGCGTTCAAACGATAATGAGCATCGAAGAAAATGGTGGCCTACGAG
| |||| | | ||| || || ||| | | || || || | | | | | | ||| || | | ||| ||||||||| | || || |||||||| ||| |||||||||||| || |||| ||||| |||||||| ||||||||||| ||||| ||||||||| |||| |
ttatgtgggtaatgaattttaatctactattgcttattgttggtggccatttcttctgaaatttaagactgataatttttacacttgctgcc--tgttttagGTGGCTACGAAGACTGAGTCAAATAAAGTTGCAGGGAATGCCATTTTATATGAATGTGTTCAAACAATAATGAGCATTGAAGATAATGGTGGCTTACGTG
upper sequence: AT1G60070.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 5
tttgtgaaatttgctttgaaaacgcttttgatctacatcagtcaggatcgtaattgcagataatcatttttgattcctaagttgattt-ttaatgtattagGTGGCATCAAAAACCGAGTCAAACAAAAATGCAGGGAATGCTATCCTATACGAATGCGTTCAAACGATAATGAGCATCGAAGAAAATGGTGGCCTACGAG
|||||| | |||| | | || | | | || | | | || | | | | | ||| | | || | || | | ||||||||| ||||||| ||||||||||||||||| |||||||| || | || ||||| ||| |||| || |||||||| ||||| | | ||||| |||| |
tttgtgcatgctgctattatttacctagaaaaaaatacgctgcataaatg-gacaaagtttacttactgtggtttcatgacatgctacattccttttctagGTGGCAACAAAAACTGAGTCAAACAAAAATGCTGGGAATGCCATTTTGTATGAATGTGTTGAAACTATTATGAGCATTGAAGATACTAGTGGCTTACGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcgtaattgcagataatcatttttgattcctaagttgatttttaatgtattagGTGGCATCAAAAACCGAGTCAAACAAAAATGCAGGGAATGCTATCCTATACGAATGCGTTCAAACGATAATGAGCATCGAAGAAAATGGTGGCCTACGAG
ttttaat putative branch site (score: 3)
taagttgatttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtgaaatttgctttgaaaacgcttttgatctacatcagtcaggatcgtaattgcagataatcatttttgattcctaagttgatttttaatgtattagGTGGCATCAAAAACCGAGTCAAACAAAAATGCAGGGAATGCTATCCTATACGAATGCGTTCAAACGATAATGAGCATCGAAGAAAATGGTGGCCTACGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG