Sequence
atgc intronic sequence ATGC exonic sequencegtcagtactggtttataatgcttagtcataattttctcttgccctcatagcaatcctaattttacatatgttgtcccatagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60040.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os04g41490.1 (Oryza sativa), 3'ss of exon 10
--gtcagtactggtttataatgct-tagtcataattttctcttgc--cctcatagcaatcctaattttacatatgttgtcccatagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
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gtataaattgctcttcattacactgcacccgctacatgaaaatgttacctcatattggtccct-tgctctttgtatttaatcacagGCTAGGATTATGCCCTGGAGAACACTAAGGTTTAACGAGTCTGTCTGTAACCCATATAATGCTGATTTTGATGGCGATGAGATGAATTTGCATGTTCCTC
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA11G15530.1 (Glycine max), 3'ss of exon 8
gtcagtactggtttataatgcttagtcataattttctcttgccctcatagcaatcctaattttacatatgttgtcccat--agGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
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----gtaatttcttaaaaagtgaaatgtagaattgtgagagattttgatccaattgcattaatatttaatttttcacatacagGCAAGGATTATGCCTTGGAGAACTTTAAGATTCAATGAATCTGTATGTAACCCATATAATGCTGACTTTGATGGTGATGAGATGAACTTACATGTCCCAC
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv06s0004g03740.t01 (Vitis vinifera), 3'ss of exon 10
---gtcagtactggtttataatgct----tagtcataattttctcttgccctcatagcaatc--ctaattttacatatgttgtcccatagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
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gtgattaaaactgattttaagtgtacaaataggtatcatttgaagttctttttttaacatttaattaagttttcttatttatgcatgtagGCGCGGATAATGCCTTGGAGAACATTGAGGTTTAATGAATCAGTTTGCAACCCATATAATGCAGATTTTGATGGTGATGAAATGAATATGCATGTCCCAC
upper sequence: AT5G60040.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S26_192V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------------------------------------------------gtcagtactggtttataatgcttagtcata-attttctcttgccctcatagcaatcctaattttacatatgttgtccc-----atagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
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gtaagatccttattcttttagattacatgataattttaaccttctttggaaatatgctgctag-atggatcaacattgcatcgtactggatgtatttttgtccttcctgccttgttatttctgttaacaccggcttttattacagGCAAGAATTATGCCATGGCGTACGCTTCGATTTAACGAGTCCGTTTGTAACCCGTATAATGCTGACTTCGACGGTGATGAAATGAATCTGCATGTTCCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cataattttctcttgccctcatagcaatcctaattttacatatgttgtcccatagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
tcctaat putative branch site (score: 2)
ttgtccc putative PPT
taattttacatatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtactggtttataatgcttagtcataattttctcttgccctcatagcaatcctaattttacatatgttgtcccatagGCAAGAATAATGCCTTGGAGAACGTTGAGGTTCAACGAATCGGTTTGTAACCCATATAATGCTGATTTTGATGGTGATGAGATGAACATGCACGTACCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG