Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaattgcatttgtttccttcagctagttgttgcacgattccgactttgaatatggaatttgtattcctgcagcatttatggtttctcccttattttgtttcagttttgtaatcagctgctactgttttgcagAAGGATCTTGTTATTTATGAAATGAATGTTCGTGCTTTTACTGCTGATGAATCCAGTGGGATGGACCCAGCTATAGGAGGCAGTTACCTCGGTTTCATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G09020.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G09020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G385578_T01 (Zea mays), 3'ss of exon 4
gtaaaaattgcatttgtttccttcagctagttgttgcacgattccgactttgaatatggaatttgtat-tcctgcagcatttatggtttctcccttatt-ttgtttcagttttgtaatcagctgctactgttttgcagAAGGATCTTGTTATTTATGAAATGAATGTTCGTGCTTTTACTGCTGATGAATCCAGTGGGATGGACCCAGCTATAGGAGGCAGTTACCTCGGTTTCATTG
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-----------------------------------------------------gtattaagattatttatcataatgcactaaatatctcaaacgcgtaattgtcaccacatttttgtt--------ctttaatctagACAGATCTTGTTATATATGAAATGAATGTCCGTGCCTTCACTGCGGATGAGTCAAGCAAGCTTGGTCCAGCCATTCGTGGAAGTTACCTTGGTGTCATTG
upper sequence: AT4G09020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G150796_T02 (Zea mays), 3'ss of exon 6
gtaaaaattgcatttgtttccttcagctagttgttgcacgattccgactttgaatatggaatttgtattcctgcagcatttatggtttctcccttattttgtttcagttttgtaatcagctgctactgttttgcagAAGGATCTTGTTATTTATGAAATGAATGTTCGTGCTTTTACTGCTGATGAATCCAGTGGGATGGACCCAGCTATAGGAGGCAGTTACCTCGGTTTCATTG
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-----------------------------------------------gtattaagatcttttatcaattatcatagtgcacaaaatatcccaaacacgtaattctcaccacattttcgttctttaatct-----agACAGATCTTGTTATATATGAAATGAATGTCCGTGCCTTCACTGCCGACGAGTCAAGCAGGCTTGCTCCAGCTATTCGTGGAAGTTACCTTGGTGTCATTG
upper sequence: AT4G09020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 3
gtaaaaattgcatttgtttccttcagctagttgttgcacgattccgactttgaatatggaatttgtattcctgcagcatttatggtttctcccttattttgtttcagttttgtaatcagctgctactgttttgcagAAGGATCTTGTTATTTATGAAATGAATGTTCGTGCTTTTACTGCTGATGAATCCAGTGGGATGGACCCAGCTATAGGAGGCAGTTACCTCGGTTTCATTG
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------------------cctgatgtctagtcttca------tttgactgagaatatg---tttctggctgaatgaagtctaatgtatgctcttccattttcatcatttttgtg----gctgctaata-----cagAAAGATCTTGTTATATATGAGATGAATGTCCGTGCATTTACAAGTGATGAATCTAGTGGTTTGGATAGCAACATTCGTGGCAGCTACCTCGGTATGATTG
upper sequence: AT4G09020.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g06520.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------gtaaaaatt--------gcatttgtt-tccttc-agctagttgttgcacgattccgactttgaatatggaatttgtattcctgcagca-tttatggtttctcccttattt---tgtttcagttttgtaatcagctgctactgt-tttgcagAAGGATCTTGTTATTTATGAAATGAATGTTCGTGCTTTTACTGCTGATGAATCCAGTGGGATGGACCCAGCTATAGGAGGCAGTTACCTCGGTTTCATTG
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gtaatttagtggggcttaaatgcattatctcagttgtgacatgcaaaagaaattctttttctgcatatgttgtcctacgagatacaaatctgacagctctctctctctctctccccctccctcttcccccccactttccagtttgtgttttagttgtatatcttgaccttattattt-ttgctattgtctttgcagAAAGATCTTGTTATATATGAGATGAATGTTCGTGCATTTACAGCTGATAAATCTAGTGGATTGGATCCAAATGTCCGTGGCAGCTACCTTGGTGTGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggtttctcccttattttgtttcagttttgtaatcagctgctactgttttgcagAAGGATCTTGTTATTTATGAAATGAATGTTCGTGCTTTTACTGCTGATGAATCCAGTGGGATGGACCCAGCTATAGGAGGCAGTTACCTCGGTTTCATTG
ctgtttt CT-rich tract
ttattttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaattgcatttgtttccttcagctagttgttgcacgattccgactttgaatatggaatttgtattcctgcagcatttatggtttctcccttattttgtttcagttttgtaatcagctgctactgttttgcagAAGGATCTTGTTATTTATGAAATGAATGTTCGTGCTTTTACTGCTGATGAATCCAGTGGGATGGACCCAGCTATAGGAGGCAGTTACCTCGGTTTCATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA