Sequence
atgc intronic sequence ATGC exonic sequencegttagtaatggcatggactaatttcccgtaacgttagttaatagttacatgaccatgtttataattgagctataaactttatatatacgtattgttagggtttctatatatattggaagtgtgaagagagtaaaacacatatattagttggaactttatgaaatataacacatgtatatataaactatgcagGAGTGGCGAAGGAGGGTAAGAAGTGTGAATACATTATTATATACGAAGACAAGGATAGAGACTGGATGCTCGTCGGAGATGTACCTTGGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52830.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G01560.1 (Glycine max), 3'ss of exon 1
gttagtaatggcatggactaatttcccgtaacgttagttaatagttacatgaccatgtttataattgagctataaactttatatatacgtattgttagggtttctatatatattggaagtgtgaagagagtaaaacacatatattagttggaactttatgaaatataacacatgtatatataaactatg-cagG---AGTGGCGAAGGAGGGTAAGAAGTGTGAATACATTATTATATACGAAGACAAGGATAGAGACTGGATGCTCGTCGGAGATGTACCTTGGCA
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--------------------------------------------------------------------------------atcaaaatctaaaaccaaaatatctctaccta------gcctcaagaaattattg-gcaatcaacaatagcgat------aattaatattcttgtttaaataaatgttgacagGCTCAGCGTTGAAGGATGAGGAGAATGTTGAACAAGTTCCCATATACGAGGACAAAGATGGTGACTGGATGCTCGTTGGAGATGTTCCTTGGGA
upper sequence: AT1G52830.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G43780.1 (Glycine max), 3'ss of exon 1
gttagtaatggcatggactaatttcccgtaacgttagttaatagttacatgaccatgtttataattgagctataaactttatatatacgtattgttagggtttctatatatattggaagtgtgaagagagtaaaacacatatattagttggaactttatgaaatataacacatgtatatataaactatgcagGAGTGGCGAAGGAGGGTAAGAAGTGTGAATACATTATTATATACGAAGACAAGGATAGAGACTGGATGCTCGTCGGAGATGTACCTTGGCA
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--------------------------------------------------------------------actagcaattcta---ataagaaaagtttaaaagtttaagttaatggcaaattggcaatcaacaatg-acg-ataataat----gttttgt----tttaaaaaatgttgaca--------gGCGAAGCGTTGAAGGATGCGGAGAATGCTGAACACGTTCCCATATACGAGGACAAAGATGGTGACTGGATGCTCGTTGGAGATGTCCCTTGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatattagttggaactttatgaaatataacacatgtatatataaactatgcagGAGTGGCGAAGGAGGGTAAGAAGTGTGAATACATTATTATATACGAAGACAAGGATAGAGACTGGATGCTCGTCGGAGATGTACCTTGGCA
atataac putative branch site (score: 3)
tttatgaaatataaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtaatggcatggactaatttcccgtaacgttagttaatagttacatgaccatgtttataattgagctataaactttatatatacgtattgttagggtttctatatatattggaagtgtgaagagagtaaaacacatatattagttggaactttatgaaatataacacatgtatatataaactatgcagGAGTGGCGAAGGAGGGTAAGAAGTGTGAATACATTATTATATACGAAGACAAGGATAGAGACTGGATGCTCGTCGGAGATGTACCTTGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG