Sequence
atgc intronic sequence ATGC exonic sequencegtacatcctgcaaccttctttccttatgattgtgttattatcgtcaacccctgtagaactttgccacagaatgatatagacttgggtagttaccaaatgggcatgagtacactatgggatgatcattctattttcttccgcagAAAATGGAGATCCTTCCAGTTAACGATCTGGATGTTGCTCTTCACAATTTTGTGAACAAGGATGATAAACTAGCCTTCTACTCATGCGTTCAGTACAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G54260.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G54260.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA12G34750.1 (Glycine max), 3'ss of exon 10
gtacatcctgcaaccttctttccttatgattgtgttattatcgtcaacccctgtagaactttgccacagaatgatatagacttgggtagttaccaaatgggcatgagtacactatgggatg-atc---attctattttcttccgcagAAAATGGAGATCCTTCCAGTTAACGATCTGGATGTTGCTCTTCACAATTTTGTGAACAAGGATGATAAACTAGCCTTCTACTCATGCGTTCAGTACAATC
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--------------------------------------------gaatgact-tgagctttcgttaaaaaggaatatgaatatagcaa--tgttagttcagtttaattttattttttaatgtatctaaactcttaatggttttgcagAAAATGGAGATACTGCCAGTTAATGATTTGGATATTGCATTGCAAAATTTTGTGAACAAAGATGATAAAATGGCATTTTACTCTTGTGTAAAATACAATA
upper sequence: AT5G54260.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv00s0160g00370.t01 (Vitis vinifera), 3'ss of exon 3
gtacatcctgcaaccttctttccttatgattgtgttattatcgtcaacccctgtagaactttgccacagaatgatatagacttgggtagttaccaaatgggcatgagtacactatgggatgatcattctattttcttccgcagAAAATGGAGATCCTTCCAGTTAACGATCTGGATGTTGCTCTTCACAATTTTGTGAACAAGGATGATAAACTAGCCTTCTACTCATGCGTTCAGTACAATC---------
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--------------------------------------------aaattcgggtgtga--taacagaagcagtatagttatttagtcttttctttctttcacttctgggtcccttagaatga------tattcattgatgcaaaaaatgaagATCCTTCCAGTCAATGATGTGGATCTTGCATTGCACAATTTTGTCAACAAAGATGACAAAATGTCTTTCTATTCTTGTGTTCAATATAATCTGGAAGAGA
upper sequence: AT5G54260.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv19s0014g03680.t01 (Vitis vinifera), 3'ss of exon 15
gtacatcctgcaaccttctttccttatgattgtgttattatcgtcaacccctgtagaactttgccacagaatgatatagacttgggtagttaccaaatgggcatgagtacactatgggatgatcattctattttcttccgcagAAAATGGAGATCCTTCCAGTTAACGATCTGGATGTTGCTCTTCACAATTTTGTGAACAAGGATGATAAACTAGCCTTCTACTCATGCGTTCAGTACAATC
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-------------------------------ggataagtggcattcaggtgtgacaacggaagcaatatagttatttaatcttttctttctttcacttc----tgggtccctga--gaatga------tacttattgatgcagAAAATGGAGATCCTTCCAGTCAATGATTTGGATGTTGCATTGCACAATTTTGTCAACAAAGATGACAAAATGGCTTTCTATTCTTGTGTTCAATATAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaccaaatgggcatgagtacactatgggatgatcattctattttcttccgcagAAAATGGAGATCCTTCCAGTTAACGATCTGGATGTTGCTCTTCACAATTTTGTGAACAAGGATGATAAACTAGCCTTCTACTCATGCGTTCAGTACAATC
tcattctattttcttc CT-rich tract
attctatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatcctgcaaccttctttccttatgattgtgttattatcgtcaacccctgtagaactttgccacagaatgatatagacttgggtagttaccaaatgggcatgagtacactatgggatgatcattctattttcttccgcagAAAATGGAGATCCTTCCAGTTAACGATCTGGATGTTGCTCTTCACAATTTTGTGAACAAGGATGATAAACTAGCCTTCTACTCATGCGTTCAGTACAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG