Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttctcttttcaaaatgattttgttttttgggatgtgttaaaacatagctgagaactaattcaggttattgatgttttgatcagACGACATTCAATGGGCGGGTTTTCATGACACATGCAACAAAGGCCATCTACAAGCTGTTGCTTACAGATTATGTAAAAGTGAGCAAAGTGTCTGTGGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G61010.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G61010.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g63590.1 (Oryza sativa), 3'ss of exon 3
gtt-tgtttctcttttcaaaatgattttgttttt-tgggatgtgttaaaacatagctgagaactaattcag---------gttattgatgttttgat--cagACGACATTCAATGGGCGGGTTTTCATGACACATGCAACAAAGGCCATCTACAAGCTGTTGCTTACAGATTATGTAAAAGTGAGCAAAGTGTCTGTGGAAG
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gtaatgttccaccatcttccgtttttttgcttcgacagtaagtgctcagctattgccctgataccattcagcatcctcaagttgctctggttttatttgcagACGACATTCAAGGGGCGCGTGTTCATGACCCATGCCACAAAGGCCATCTACAGGCTGCTCCTTTCCGATTATGTCAAAGTCAGCAAAGTTTCTGTGGAGG
upper sequence: AT1G61010.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G422649_T01 (Zea mays), 3'ss of exon 3
-----gtttgtttctcttttcaaaatgattttgttttttgggatgtgttaaaacatagctgagaactaattcaggttattgatgttttgatcagACGACATTCAATGGGCGGGTTTTCATGACACATGCAACAAAGGCCATCTACAAGCTGTTGCTTACAGATTATGTAAAAGTGAGCAAAGTGTCTGTGGAAG
| || ||| | || | || | || | ||| | ||| | || || | | ||||||| ||||| || ||||| || ||||| || ||||| || || |||||||| || ||||||||| |||| | |||||||| ||||| ||||||||||| ||||| |
gtaatgactgcgcatctgcgttac-tggtgctgcgtgtttgt-tgttgtggtgcattttttttgctgaaatctgcca---ggtgttttgtgcagACCACGTTCAAGGGCCGGGTGTTTATGACCCACGCCACAAAGGCTATTTACAAGCTGCTGCTCTCGGATTATGTCAAAGTCAGCAAAGTGTCCGTGGAGG
upper sequence: AT1G61010.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ04498 (Selaginella moellendorffii), 3'ss of exon 3
gtttgtttctcttttcaaaatgattttgttttttgggatgtgttaaaacatagctgagaactaattcaggttattgatgttttgatcagACGACATTCAATGGGCGGGTTTTCATGACACATGCAACAAAGGCCATCTACAAGCTGTTGCTTACAGATTATGTAAAAGTGAGCAAAGTGTCTGTGGAAG
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-------------------------------------gtacttgatttcttttttgcgaggctggtttgtaaagttttgtctc--tcagACCACATTCAAAGGCCGAGTGTTCATGACACACGCAACCAAAGCCATTTACAAGCTTTTGCTCACGGACTATGTCAAGATCAGCAAAGGGTCTGTCGAAG
upper sequence: AT1G61010.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ12712 (Selaginella moellendorffii), 3'ss of exon 5
gtttgtttctcttttcaaaatgattttgttttttgggatgtgttaaaacatagctgagaa-ctaattcaggttattgatgttttgatcagACGACATTCAATGGGCGGGTTTTCATGACACATGCAACAAAGGCCATCTACAAGCTGTTGCTTACAGATTATGTAAAAGTGAGCAAAGTGTCTGTGGAAG
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-------------------------------------gtacttgagttctcttttgcgaggctggttta---taaagttttgtctctcagACCACATTCAAAGGCCGAGTGTTCATGACACACGCAACCAAAGCCATTTACAAGCTTTTGCTCACGGACTATGTCAAGATCAGCAAAGGGTCTGTCGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggatgtgttaaaacatagctgagaactaattcaggttattgatgttttgatcagACGACATTCAATGGGCGGGTTTTCATGACACATGCAACAAAGGCCATCTACAAGCTGTTGCTTACAGATTATGTAAAAGTGAGCAAAGTGTCTGTGGAAG
ttaaaacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttctcttttcaaaatgattttgttttttgggatgtgttaaaacatagctgagaactaattcaggttattgatgttttgatcagACGACATTCAATGGGCGGGTTTTCATGACACATGCAACAAAGGCCATCTACAAGCTGTTGCTTACAGATTATGTAAAAGTGAGCAAAGTGTCTGTGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG