Sequence
atgc intronic sequence ATGC exonic sequence...cgtggcttttaacctgaaaattgtcactgtctaagtcaattctatcacatcacttacctctaattttattttgctaattaaataaatgaatataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------------------cgtggcttttaacctgaaaattgtcactgtctaagtcaattctatcacatcacttacctcta--attttattttg-ctaattaaataaatgaata-taatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
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gtgtttttctcttgttggagtattactaattttatttttttcgtaacactttgaatgaatttgcattttctggaatcaatatgctaataaatatttttttttaactttaacacg-catatcatcaacttctatcatatcattttggctaattaaat---tgtataacaatttagAGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGTATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCC
upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA05G34180.1 (Glycine max), 3'ss of exon 11
cgtggcttttaacctgaaaattgtcactgtct-aagtcaattctatcacatcacttacctctaattttattttgctaattaaataaatgaatataatat-agAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
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--taatgtacagcttcataatgttttctttctcaagattattcttttctattaaacatttggattgcctgatcacttagaaagtttttctttgttttcttagAGAAGAGGAAGGGCTGGTCGTGTTCAACCTGGTGAATGCTACCATCTTTATCCCAGATGTGTTTATGATGCTTTTGCTGATTATCAATTGCCAGAGCTTT
upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G05480.1 (Glycine max), 3'ss of exon 11
cgtggcttttaacctgaaaattgtcactgtctaagtcaattctatcacatcacttacctctaattttattttgctaattaaataaatgaatataatat-agAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
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gttaatgtacagcttcataatgttttctttctcagatttttctttc-tattaaacatttagactacctggtcgcttataaagtttttgtttattttcttagAGAAGAGGAAGGGCTGGTCGTGTTCAGCCTGGTGAATGCTACCATCTTTATCCCAGATGTGTTTATGATGCTTTTGCTGATTATCAATTGCCAGAGCTTT
upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv17s0000g03030.t01 (Vitis vinifera), 3'ss of exon 10
---cgtggcttttaacctgaaaattgtcactgtctaagtcaattctatcacatcacttacctctaattttattttgctaattaaataaatgaatataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
| | | | | || | | | | || | | || | || | ||| | ||| || ||| | | || | |||||||| ||||| |||| || || || ||||| || || || |||||||| |||||| ||||||||||||||| ||| |||| ||||| || ||||||||||
gggtttaagcagtttcttacatatcattttgcttttgtacgatgttttgggatttatcacatg-gattaaagtttactgatttgctc--ttcattttttatagAGAAGAGGAAGAGCGGGTCGTGTACAACCTGGTGAATGTTACCATCTGTATCCAAAATGTGTATATGATGCTTTTTCTGATTACCAATTGCCAGAACTTC
upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 11
cgtggcttttaacctgaaaattgtcactgtctaagtcaattcta-tca------catcacttacctctaattttattttgctaattaaataaatgaatataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
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-----ctgattccttccaaatta-cattgacttagaaaataggaatcaagggtttattgcatatgtttgatat-attttcctttcctatgctttgtctaatatgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacatcacttacctctaattttattttgctaattaaataaatgaatataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
tgctaat putative branch site (score: 2)
taattttattttgcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgtggcttttaacctgaaaattgtcactgtctaagtcaattctatcacatcacttacctctaattttattttgctaattaaataaatgaatataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
- - - - - -acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa