Sequence
atgc intronic sequence ATGC exonic sequencegtcatcatcatagacttcttcgtttttttttccaattttggattcttaatctctcacaatacttaaaaatccgatctttcagATACTTGGAACTGGAATGGATACACAGGATACATCATCTTCTGTATTACTCTTCTTTGATAAGCAAAGATTCATCTTTAATGCTGGAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52160.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g13150.1 (Oryza sativa), 3'ss of exon 3
----------------gtcatcatcatagacttcttcgtttttttttccaattttggattcttaatctctcacaatactta--aaaatccgatctttcagATACTTGGAACTGGAATGGATACACAGGATACATCATCTTCTGTATTACTCTTCTTTGATAAGCAAAGATTCATCTTTAATGCTGGAGAG
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tcagttaatcaaccccctcacttagatcaactcatgggaacagggacaaatgcctttgccagtgatcttaccccttcgttcttggcttcttgctgtgcagATACTTGGTACAGGAATGGACACACAAGATACTTCACCTTCCATTTTACTCTTCTTTGACAAACAGAGGTTTATATTTAATGCTGGCGAG
upper sequence: AT1G52160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G379286_T01 (Zea mays), 3'ss of exon 1
-----------gtcatcatcatagacttcttcgttttt-------ttttccaattttggattcttaatctctcacaatacttaaaaatccgatctttcagATACTTGGAACTGGAATGGATACACAGGATACATCATCTTCTGTATTACTCTTCTTTGATAAGCAAAGATTCATCTTTAATGCTGGAGAG
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tgtgggggcaatttcttcccttgaactagttcatgagtgcaggaactgttgttcttttggttttcattcaatctcactcccctttgttattcctgcgcagATACTTGGTACAGGAATGGACACACAGGACACTTCACCTTCTATTCTACTATTCTTTGACAAACAAAGGTTTATTTTTAATGCGGGCGAG
upper sequence: AT1G52160.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0002g04000.t01 (Vitis vinifera), 3'ss of exon 1
-------------gtcatcatcatagacttcttcgtttttttttccaa----ttttg-gattcttaatctctcacaatacttaaaaatccgatctttcagATACTTGGAACTGGAATGGATACACAGGATACATCATCTTCTGTATTACTCTTCTTTGATAAGCAAAGATTCATCTTTAATGCTGGAGAG
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tcaaaattttggggaacccaacatagcttaaaagtttgaagtatccaagatgtcttgtggttaaaaatatttgatatcttcttacttgctatgattgcagATTCTGGGGACTGGGATGGATACACAAGATACTTCGTCTTCTGTCTTGCTTTTCTTTGATAAACAAAGATTTATTTTCAATGCTGGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttccaattttggattcttaatctctcacaatacttaaaaatccgatctttcagATACTTGGAACTGGAATGGATACACAGGATACATCATCTTCTGTATTACTCTTCTTTGATAAGCAAAGATTCATCTTTAATGCTGGAGAG
ctctcac putative branch site (score: 3)
tctttc putative PPT
acaatacttaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcatcatcatagacttcttcgtttttttttccaattttggattcttaatctctcacaatacttaaaaatccgatctttcagATACTTGGAACTGGAATGGATACACAGGATACATCATCTTCTGTATTACTCTTCTTTGATAAGCAAAGATTCATCTTTAATGCTGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA