Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagcaagtcattgttagtataaaatcttaatggtctatagattgtgatttgctgaaatgtctaataagtatgtcaccattctacagATATCTGAAGAAAGCGAGTACGATCCTCTTGATCTCTTCTCTGGATCAAAAGAGAGTGTTTTGGAAGCTATAAAAGCTTTATATTCCACTCCTCAAAACA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42810.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G067299_T02 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------------------------------------gtaaaagcaagtcattgttagta----taaaatctta-atggtctatagattgtgatttgctga--aatgtctaataagtatgtcaccattctacagATATCTGAAGAAAGCGAGTACGATCCTCTTGATCTCTTCTCTGGATCAAAAGAGAGTGTTTTGGAAGCTATAAAAGCTTTATATTCCACTCCTCAAAACA
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gtgtgtagattggaatgcttgatccaagataaaattccactctcttttgcgcacttaataacatccatcgatgatacaaacttgatcaaaataccttaaggcttgctatttacggcactcttgtaatattataccgtctcttgctttttgacatcaggttgattcccaatacattcttgcacacatttcagATATCGAAGACTAGTGAGTACAATCCTCTTGATCTATTTTCTGGGTCAAAAGAGAGAATATGCATGGCCATCAAGTCCCTTTTCTCAACTCCTCAGAACA
upper sequence: AT5G42810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G067299_T06 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------------------------------------gtaaaagcaagtcattgttagta----taaaatctta-atggtctatagattgtgatttgctga--aatgtctaataagtatgtcaccattctacagATATCTGAAGAAAGCGAGTACGATCCTCTTGATCTCTTCTCTGGATCAAAAGAGAGTGTTTTGGAAGCTATAAAAGCTTTATATTCCACTCCTCAAAACA
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gtgtgtagattggaatgcttgatccaagataaaattccactctcttttgcgcacttaataacatccatcgatgatacaaacttgatcaaaataccttaaggcttgctatttacggcactcttgtaatattataccgtctcttgctttttgacatcagGTTGATTCCCAATACATTCTTGCACACATTTCAGATATCGAAGACTAGTGAGTACAATCCTCTTGATCTATTTTCTGGGTCAAAAGAGAGAATAT-GCATG--------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtctatagattgtgatttgctgaaatgtctaataagtatgtcaccattctacagATATCTGAAGAAAGCGAGTACGATCCTCTTGATCTCTTCTCTGGATCAAAAGAGAGTGTTTTGGAAGCTATAAAAGCTTTATATTCCACTCCTCAAAACA
gtctaat putative branch site (score: 3)
ccattct putative PPT
taataagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagcaagtcattgttagtataaaatcttaatggtctatagattgtgatttgctgaaatgtctaataagtatgtcaccattctacagATATCTGAAGAAAGCGAGTACGATCCTCTTGATCTCTTCTCTGGATCAAAAGAGAGTGTTTTGGAAGCTATAAAAGCTTTATATTCCACTCCTCAAAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC