Sequence
atgc intronic sequence ATGC exonic sequencegttagccaaaatccttgtccttcaattgagcatcgattcaaaagctgtctgattactccaattaacactaatactttgttaaaagatgcttgtttattcatgacttcatacctaacagagaatttccgatagGTTGGGTTTAAAGTTCGTCTAGAAGGAATGAGAGGAAAGAATACCCACCTTCTATTTTGTACAAGTGGTATCCTTCTCAGACGGCTGCTTAGTGATCGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04895.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04895.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G29910.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------gttagccaaaatccttgtccttcaattgagcatc-gattcaaaagctgtctgattactccaattaacactaatactttgttaaaagatgcttgtttattcatgacttcatacc-taacagagaatttccgatagGTTGGGTTTAAAGTTCGTCTAGAAGGAATGAGAGGAAAGAATACCCACCTTCTATTTTGTACAAGTGGTATCCTTCTCAGACGGCTGCTTAGTGATCGCA
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gtaagccctgtttttctggaaatggacaaaagaacaaatgcatgtaatagtacaaaaaacatgggtgcaaatattagtattcatgaagaaaataaaagattcataaactacttttttgctcttg-----aatgggattttaaaatttggaatatttttgttcttgctgctataccacaacagaggttttttgatagGTTGGCTTCGAAGTTCGACTAGAAGGAATGAAAGGAAAAAACACCCATCTGCTATTTTGTACCAGTGGTATATTACTTAGAAGGTTGTTGAGTGATCGAA
upper sequence: AT5G04895.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G24630.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------gttagccaaaatccttgtccttcaattgagcatc-gattcaaaagctgtctgattactccaattaacactaatactttgttaaaagatgcttgtttattcatgacttcatacc-taacagagaatttccgatagGTTGGGTTTAAAGTTCGTCTAGAAGGAATGAGAGGAAAGAATACCCACCTTCTATTTTGTACAAGTGGTATCCTTCTCAGACGGCTGCTTAGTGATCGCA
| || || || || | | | || | | |||||| || || | || ||| | | | ||| | | | ||| ||| || ||||| ||||||| ||| |||||||||| || |||||||| |||||||||||| |||||| || ||||| || ||||||||||| |||||||| | || ||| ||||| | |||||||| |
gtaagccctgtttttctggaaatggacaaaagtacaaatgcatgcaatagtacagaaaacatgggtgcaaatattattattcatgaagaaaataaaagattcataaactacttttttgctcttg-----aatgggattttaaaatttggaatatttttgttcttgctgctataccacaacagaggttttttgatagGTTGGCTTCAAAGTTCGATTAGAAGGAATGAAAGGAAAAAACACCCATCTGCTATTTTGTACCAGTGGTATATTACTTAGAAGGCTGTTGAGTGATCGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaaaagatgcttgtttattcatgacttcatacctaacagagaatttccgatagGTTGGGTTTAAAGTTCGTCTAGAAGGAATGAGAGGAAAGAATACCCACCTTCTATTTTGTACAAGTGGTATCCTTCTCAGACGGCTGCTTAGTGATCGCA
acctaac putative branch site (score: 2)
tttcc putative PPT
ttgtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagccaaaatccttgtccttcaattgagcatcgattcaaaagctgtctgattactccaattaacactaatactttgttaaaagatgcttgtttattcatgacttcatacctaacagagaatttccgatagGTTGGGTTTAAAGTTCGTCTAGAAGGAATGAGAGGAAAGAATACCCACCTTCTATTTTGTACAAGTGGTATCCTTCTCAGACGGCTGCTTAGTGATCGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT