Sequence
atgc intronic sequence ATGC exonic sequencegtaagatcactctctcttacttgcatcatatgttgataacaaccatttctctgtagacttagtattcatttcaactcagaactactctcctgaactgtttcatctcttgggaaacttttagctgatgcagtatttgaattgactcgttttcagGTCAACCTACTATGCTGCTACAGATGTGGTTATTCTCAGATTTATGATTGAGGCTTGTTGGGCTCCTATGCTTGCTGCATTCAGTGTGCCGCTAGACCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G60860.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 5
-------------------------gtaagatcactctctct-tacttgcatcatatgttgataacaaccatttctctgtagacttagtattcatttcaactcag-aactactctcctgaactgtttcatctcttgggaaacttttagctgatgcagtatttgaattgactcgttttcagGTCAACCTACTATGCTGCTACAGATGTGGTTATTCTCAGATTTATGATTGAGGCTTGTTGGGCTCCTATGCTTGCTGCATTCAGTGTGCCGCTAGACCAG
| || ||| | || | ||| | ||||| ||||| ||| || | ||||| | || | |||||| | | |||| || |||| || || |||| || | | | ||||| | |||||||| | |||| | || |||||||| || || | | ||| ||| | |||| ||| |||||||||||||||||||| |||||||| || || ||||||
gtaagtcatgctagatgtctagatggatagctcaatacctgtatacactaaatgcatgttttccttggtcatttttct------ttgctgcccatttgatttctgcaactacattattttactgatttgtctcatgtcaattatttatctagaatattttatgaatgaa-------tcagGTCAGTATTCTATCCAGCAACAGATGTAGTAGTTTTGAAATTCATGGTCGAGGTTTGCTGGGCTCCTATGCTTGCTGCCTTCAGTGTTCCACTTGACCAG
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 5
----------------------gtaagatcactctctcttacttgcatcatatgttgataacaaccatttctctgtagacttagtattcatttcaactcagaactactctcctgaactgtttcatctcttggga---aactt-ttagctgatgcagtatttgaattgactcgtttt--------cagGTCAACCTACTATGCTGCTACAGATGTGGTTATTCTCAGATTTATGATTGAGGCTTGTTGGGCTCCTATGCTTGCTGCATTCAGTGTGCCGCTAGACCAG
||| | ||| | | | | | | | ||| | | || | ||| || || | || | | | ||| || | | | | || || | || | ||| || | | |||| |||||| | ||| | || |||||||| ||| || | | || ||| |||||| ||| ||||||||||||||||| ||||||||||| || || ||||||
gtaagttattagatgttgagatgtatagtggtatcggcttggctagaccgctagattaagattcttgttttatttcaacatt--ttttctgttttgctaacaatatatttagggtcttgtagtatgtttcgacatttaatttatcagttaatgttttaactatgacttttttttttggaacaaccagGTCTGTATTTTATCCAGCCACAGATGTAGTTGTTTTGAAGTTCATGGTTGAGGTTTGCTGGGCTCCTATGCTTGCAGCATTCAGTGTTCCACTTGACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcatctcttgggaaacttttagctgatgcagtatttgaattgactcgttttcagGTCAACCTACTATGCTGCTACAGATGTGGTTATTCTCAGATTTATGATTGAGGCTTGTTGGGCTCCTATGCTTGCTGCATTCAGTGTGCCGCTAGACCAG
aattgac putative branch site (score: 3)
ctcgttttc CT-rich tract
tatttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatcactctctcttacttgcatcatatgttgataacaaccatttctctgtagacttagtattcatttcaactcagaactactctcctgaactgtttcatctcttgggaaacttttagctgatgcagtatttgaattgactcgttttcagGTCAACCTACTATGCTGCTACAGATGTGGTTATTCTCAGATTTATGATTGAGGCTTGTTGGGCTCCTATGCTTGCTGCATTCAGTGTGCCGCTAGACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC