Sequence
atgc intronic sequence ATGC exonic sequencegtaacgagcccttgatgtacatcacatttttttttgtattcaaccgcattctcttatcatcagctttgttccttagaaatatagagagtatataacacatgtaattaagttttacttatgcagGGTCGTCTTTTCCTGTCTGCAAGAATTGTTGGCTTTTATGCAAGCATTTTTGGTAACAAAACAAAATTCTTTTTCCTGTGGGAAGATATAGAGGAAATTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03370.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g19400.1 (Oryza sativa), 3'ss of exon 5
gtaacgagcccttgatgtacatcacatttttttttgtattcaaccgcattctcttatcatcagctttgttccttagaaatatagagagtatataacacatgtaattaagttttacttatgcagGGTCGTCTTTTCCTGTCTGCAAGAATTGTTGGCTTTTATGCAAGCATTTTTGGTAACAAAACAAAATTCTTTTTCCTGTGGGAAGATATAGAGGAAATTC
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----------tttgtcacatagc-catattactgcacaaccaa--gttagacattaagatctttttttttgtctgtgaacttgcatggtagctgacgcttgtgtctgt----------tgcagGGCCGCCTGTTTTTATCTCCAAGAATTATTGGGTTCTACACTAATCTTTTTGGCCACAAAACAAAATTCTTCTTTCTTTGGGAAGATATCGAGGACATCC
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G027665_T01 (Zea mays), 3'ss of exon 5
gtaacgagcccttgatgtacatcacatttttttttgtattcaaccgcattctcttatcatcagctttgttccttagaaatatagagagtatataacacatgtaattaagttttacttatgcagGGTCGTCTTTTCCTGTCTGCAAGAATTGTTGGCTTTTATGCAAGCATTTTTGGTAACAAAACAAAATTCTTTTTCCTGTGGGAAGATATAGAGGAAATTC
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---tctaatcaacgat-tacttaagggtataactgttactttacaacaaactc--aacataacctttttattttatcaaactaaatcatgtctgcc-tgtgt----------------tgcagGGTCGTCTTTTTCTATCTCCAAGAATATTTGGGTTTTACACAAATATTTTTGGCCACAAAACAAAATTCTTCTTACTTTGGGAAGATATTGAAGACATTT
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G005195_T02 (Zea mays), 3'ss of exon 5
gtaacgagcccttgatgtacatcacatttttttttgtattcaacc--gcattctcttatcatcagctttgttccttagaaatatagagagtatataacacatgtaattaagttttacttatgcagGGTCGTCTTTTCCTGTCTGCAAGAATTGTTGGCTTTTATGCAAGCATTTTTGGTAACAAAACAAAATTCTTTTTCCTGTGGGAAGATATAGAGGAAATTC
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---gtgattacttaagg-gcatcac-tgttactttacaacaaactaagcataaccttttcat-gtcatcatgcctgagaactaaat-----------catgtctgcctgtgtt--------gcagGGTCGTATTTTTCTATCTCCAAGAATATTTGGGTTTTACACAAATCTTTTTGGCCACAAAACAAAATTCTTCTTTCTTTGGGAAGATATTGAAGACATCC
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 5
gtaacgagcccttgatgtacatcacatttttttttgtattcaaccgcattctcttatcatcagctttgttccttagaaatatagagagtatataaca------catgtaattaagttt-tacttatgcagGGTCGTCTTTTCCTGTCTGCAAGAATTGTTGGCTTTTATGCAAGCATTTTTGGTAACAAAACAAAATTCTTTTTCCTGTGGGAAGATATAGAGGAAATTC
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--------------gtgtggttattctgttatgtgatgttgaaattcatggtcaattattctactttggtttttactggtgcatgcttcttttagtatcttctcataaaattgtgaatatttctctgcagGGCCGCCTATTTCTATCAGCAAGAATAATTGGATTTCATGCAAATTTGTTTGGAAACAAGACAAAATTCTTTTTTCTTTGGGAAGATATTGAAGAAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccttagaaatatagagagtatataacacatgtaattaagttttacttatgcagGGTCGTCTTTTCCTGTCTGCAAGAATTGTTGGCTTTTATGCAAGCATTTTTGGTAACAAAACAAAATTCTTTTTCCTGTGGGAAGATATAGAGGAAATTC
atataac putative branch site (score: 3)
ttttactt putative PPT
atgtaattaagtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacgagcccttgatgtacatcacatttttttttgtattcaaccgcattctcttatcatcagctttgttccttagaaatatagagagtatataacacatgtaattaagttttacttatgcagGGTCGTCTTTTCCTGTCTGCAAGAATTGTTGGCTTTTATGCAAGCATTTTTGGTAACAAAACAAAATTCTTTTTCCTGTGGGAAGATATAGAGGAAATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA