Sequence
atgc intronic sequence ATGC exonic sequence...atgaaggaatgtatgatgattatatttgcttggtaatgcgaagcaagctactttatccattgcaaccaggtgaagataaatatcagtatcttttttacagGTACGAGATCCAATGCCAGCAGTATATTTCTTCCTCATTGATGTCTCAATGAACGCGATTCAAACAGGTGCAACTGCAGCTGCTTGCAGTGCAATCCAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G44340.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g24250.1 (Oryza sativa), 3'ss of exon 6
---atgaaggaatgtatgatgattatatttgcttggtaatgcgaagcaagctactttatccattgcaaccaggtgaagataaatatcagtatct-tttttacagGTACGAGATCCAATGCCAGCAGTATATTTCTTCCTCATTGATGTCTCAATGAACGCGATTCAAACAGGTGCAACTGCAGCTGCTTGCAGTGCAATCCAGC
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tgtatctgctgaactttcac-attctagtt--tcagtaatatattttataatttcactttgataacattgtattaatgataa-tgtaatcttcaaccttttcagGTTCGTGATCCAATGCCAGCTGTGTATTTTTTCCTCATTGATGTCTCCATGAATGCCATACAGACTGGTGCAACAGCTGCAGCTTGCAGTGCAATTTCCC
upper sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os11g29200.1 (Oryza sativa), 3'ss of exon 6
atgaaggaatgtatgatgattatatttgcttggtaatgcga--agcaagctactttatccattgcaaccaggtgaagataaatatcagtatcttt--------tttacagGTACGAGATCCAATGCCAGCAGTATATTTCTTCCTCATTGATGTCTCAATGAACGCGATTCAAACAGGTGCAACTGCAGCTGCTTGCAGTGCAATCCAGC
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----------gtttgtcatcagcgatcgctagatcatataactacagacctgctgttgcatttgattcttgattacgaacaatactaatattatcataataaactttcagGTTCGCGACCCGATGCCTGCTGTATATTTCTTTCTTATTGATGTCTCCATGAATGCTATACAAACAGGTTCAACTGCTGCAGCTTGCAGTGCGATTTCCC
upper sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G075680_T01 (Zea mays), 3'ss of exon 6
---atgaaggaatgtatgatgattatatttgcttggtaatgcgaagcaagctactttatccat-tgcaaccaggtgaagataaatatcagtatcttttttacagGTACGAGATCCAATGCCAGCAGTATATTTCTTCCTCATTGATGTCTCAATGAACGCGATTCAAACAGGTGCAACTGCAGCTGCTTGCAGTGCAATCCAGC
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tccatcagccaatctagtgccctgttttattttttgtt-tcttatttactttaccttttgcttgtactattcattgagaatgcataatcataattttt---cagGTTCGTGATCCAATGCCTGCTGTATACTTCTTCCTTATTGATGTCTCTATGAATGCTATACAAACTGGTGCAACTGCTGCAGCTTGCAGTGCTATTTCTC
upper sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G019236_T08 (Zea mays), 3'ss of exon 6
----atgaaggaatgtatgatgattatatttgcttggtaatgcgaagcaagctactttatccat-tgcaaccaggtgaagataaatatcagtatcttttttacagGTACGAGATCCAATGCCAGCAGTATATTTCTTCCTCATTGATGTCTCAATGAACGCGATTCAAACAGGTGCAACTGCAGCTGCTTGCAGTGCAATCCAGC
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gttcattggccaatccagtgcgctcttgtattttttgtt-tcttatttacttcgccgtttgcttatactgttcagtgagaatc--catcaaaataatttt--cagGTTCGTGATCCAATGCCTGCTGTATACTTCTTCCTTATTGATGTCTCCATGAATGCTATACAAACTGGTGCAACTGCTGCAGCTTGCAGTGCTATTTCCC
upper sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G24330.1 (Glycine max), 3'ss of exon 8
--atgaaggaatgtatgatga-ttatatttgcttggtaatgcgaagcaagctactt-tatccattgcaaccaggtgaagataaatatcagtatcttttttacagGTACGAGATCCAATGCCAGCAGTATATTTCTTCCTCATTGATGTCTCAATGAACGCGATTCAAACAGGTGCAACTGCAGCTGCTTGCAGTGCAATCCAGC
||| | | | || | || ||| | || || | | | | | | || | | | | | | | || ||| ||| | |||| || ||||||||||| || ||||| ||||| ||||||||||| || ||||| || ||||||| |||||||| || || ||||||||||| || |
ttatgcttcagtctggaataagttttatatttctgttattcttgattcttcaattagtgtctgtgatgatgactggtgtgtgatt--cactat--tttctgtagGTCCGTGATCCAATGCCTGCTGTATACTTCTTTCTCATTGATGTATCCATGAATGCTGTTCAAACTGGTGCAACAGCTGCAGCTTGCAGTGCCATAACTC
upper sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G42720.1 (Glycine max), 3'ss of exon 8
atgaaggaatgtatgatgattatatttgcttggtaatgcgaagcaagctactttatccattgcaaccaggtgaagataaatatcagtatc----ttttttacagGTACGAGATCCAATGCCAGCAGTATATTTCTTCCTCATTGATGTCTCAATGAACGCGATTCAAACAGGTGCAACTGCAGCTGCTTGCAGTGCAATCCAGC
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ataattctttatcct-tactcatttttactt--ttctgttattcttgtttcttcaattaatgtctgt-gatgatgactggcgtgtgattcactattttctgtagGTCCGTGAGCCCATGCCTGCTGTGTACTTCTTTCTCATTGATGTATCCATGAATGCTGTTCAAACTGGTGCAACAGCTGCAGCTTGCAGTGCCATAAGTC
upper sequence: AT3G44340.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv19s0014g05310.t01 (Vitis vinifera), 3'ss of exon 7
atgaaggaatgtatgatgattatatttgcttggtaatgcgaagcaagctactttatccat-tgcaaccaggtgaagataaatat-cagtatcttttttacagGTACGAGATCCAATGCCAGCAGTATATTTCTTCCTCATTGATGTCTCAATGAACGCGATTCAAACAGGTGCAACTGCAGCTGCTTGCAGTGCAATCCAGC
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--gaaaccattcctcctgttctttcatcgaagttgttctttggtatgggggtttttgggtctaaagataagtaattctttgcatgctttgtcttatttccagGTGCGTGAGCCAATGCCTGCTGTGTTTTTCTTTCTGATCGATGTATCAATGAATGCAATACAGACTGGTGCAACTGCAGCAGCTTGCAGTGCAATCACTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctactttatccattgcaaccaggtgaagataaatatcagtatcttttttacagGTACGAGATCCAATGCCAGCAGTATATTTCTTCCTCATTGATGTCTCAATGAACGCGATTCAAACAGGTGCAACTGCAGCTGCTTGCAGTGCAATCCAGC
tatctttttt CT-rich tract
ataaatatcagtatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgaaggaatgtatgatgattatatttgcttggtaatgcgaagcaagctactttatccattgcaaccaggtgaagataaatatcagtatcttttttacagGTACGAGATCCAATGCCAGCAGTATATTTCTTCCTCATTGATGTCTCAATGAACGCGATTCAAACAGGTGCAACTGCAGCTGCTTGCAGTGCAATCCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- gaaggaa
- - - - - - - - - - - - - - - - - - - -gaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agataaa