Sequence
atgc intronic sequence ATGC exonic sequencegtgagtactcgttggtcttatatcggtgcttgtccgtcagttgattcacatctattcttctagggatctttctctttgatatttaactgagttctctagcatatatatgaacattgttgctctctgaaatttctcatagGACATATATTGCCTGGATGCTGATGGTGCTCTCTTTGATGCTGCTCTGCTTGCTGCTGTCGCAGCCTTCTCCAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G60080.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G60080.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G22250.2 (Glycine max), 3'ss of exon 6
---------------gtgagtactcgttgg---tcttatatcggtgcttgtccgtcagt-tgattcacatctattcttctagggatctttctctttgat--atttaactgagttctctagcatatatatgaacattgt--tgctctctgaaatttctcatagGACATATATTGCCTGGATGCTGATGGTGCTCTCTTTGATGCTGCTCTGCTTGCTGCTGTCGCAGCCTTCTCCAATC
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gttagcttttatatggacggcatttaccaaatttcacatatcagctatagaaagagtgcatagcacacctcattcggtgtgaggcactctgtctttgtttgctctgatggtgttgttattaatctat-tgaacgacagaatgctgccttctctatcatgcagGATATCTATTGTTTGGATGCTGATGGTGCTCTTTTTGATGCTGCATTAATTTCTGCAGTTGCTGCCTTATCTCATT
upper sequence: AT1G60080.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G50270.1 (Glycine max), 3'ss of exon 5
----------------------gtgagtactcgttggtcttatatcggtgcttgtccgtcagttgattcacatctattct----tctagggatctttctctttgata---tttaactgagttctctagcatatatatgaacattgt-tgctctctgaaatttctcatagGACATATATTGCCTGGATGCTGATGGTGCTCTCTTTGATGCTGCTCTGCTTGCTGCTGTCGCAGCCTTCTCCAATC
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gtaagcttgtttatggactgcattaaccaaatttcacatataaaccattgaaagaatgtatagcacaccacatttggtgtgaggtacactgactttgttagtttgtttgctctgattgtgttattatcaatctattgaatgacagaatgctgccttctttatcatgcagGATATCTATTGTTTGGATGCTGATGGTGCTCTTTTTGATGCTGCGTTACTTTCTGCCATTGCTGCCTTATCTCATT
upper sequence: AT1G60080.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0007g08550.t01 (Vitis vinifera), 3'ss of exon 6
gtgagtactcgttggtcttatatcggtgcttgtccgtcagttgattcacatctattcttctagggatctttctctttgatatttaactgagttctctagcatatatatgaacattgttgctctctgaaatttctcatagGACATATATTGCCTGGATGCTGATGGTGCTCTCTTTGATGCTGCTCTGCTTGCTGCTGTCGCAGCCTTCTCCAATC
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------------------ta-gttggtgctc-tcagtgagt-gactttagccaagt---gtgaacatcgtgcatttttttgttt--ctgtattgaatgacaaagaaat--acat--ttggtatctgg---------cagGACATATACTGTTTGGATGCAGATGGTTCTCTGTTTGATGCTGCTTTACTTGCAGCAGTGGCTGCCTTCTCTCACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactgagttctctagcatatatatgaacattgttgctctctgaaatttctcatagGACATATATTGCCTGGATGCTGATGGTGCTCTCTTTGATGCTGCTCTGCTTGCTGCTGTCGCAGCCTTCTCCAATC
atttaac putative branch site (score: 3)
tttctcat putative PPT
atatatatgaacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtactcgttggtcttatatcggtgcttgtccgtcagttgattcacatctattcttctagggatctttctctttgatatttaactgagttctctagcatatatatgaacattgttgctctctgaaatttctcatagGACATATATTGCCTGGATGCTGATGGTGCTCTCTTTGATGCTGCTCTGCTTGCTGCTGTCGCAGCCTTCTCCAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT