Sequence
atgc intronic sequence ATGC exonic sequencegtaagatatattcttgttttttccttcagtttgttaaattccatgggttctcattgaatccttgaccggacaactgaattttgcatgttgcttgtagGCTGTATACCACATGCCAACAACTGAGAATGATGCACCCACAGCAAGTATACCGTTGGCTCTCCAAAGTTTGTTTTACAAGCTCCAATACAATGACACTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06600.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 5
gtaagatatattcttgttttttccttcagtttgttaaattccatgggttctcat---tgaatccttgaccggacaactga-attttgcatgttgcttgtagGCTGTATACCACATGCCAACAACTGAGAATGATGCACCCACAGCAAGTATACCGTTGGCTCTCCAAAGTTTGTTTTACAAGCTCCAATACAATGACACTA
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----------------------------gtgaggctaaatttgtaaattctcttaaatgaatcctatgatgcgaggctgatacagagaatgatattt-tagGCTGTATACCATATGCCAACTACAGAGAATGATACACCTTGCGGGAGCATCCCTTTGGCTTTGCAAAGTCTTTTCTGCAAACTTCAGCATAGTGACAATA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 5
gtaagatatattcttgttttttccttca-gtttgttaaattccatgggttctcattgaatccttgaccggacaactgaattttgcatgttgcttgtagGCTGTATACCACATGCCAACAACTGAGAATGATGCACCCACAGCAAGTATACCGTTGGCTCTCCAAAGTTTGTTTTACAAGCTCCAATACAATGACACTA
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gtgaaatcaatcattgttctgttctacatgtttctctaagcacctgaatt----ttgaaccatttattgaa--------------atgtt-ttcatagGCTGTATATCATATGCCAACAACTGAGAATGACATGCCATCTGGGAGTATCCCTTTAGCCCTGCAGAGCCTGTTTTACAAGCTACAGTATAGTGACAACA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------gtaagatatattcttgttttttccttcagtttgttaaattccatgggttctcattgaatccttgaccggacaactgaattttgcatgttgcttgtagGCTGTATACCACATGCCAACAACTGAGAATGATGCACCCACAGCAAGTATACCGTTGGCTCTCCAAAGTTTGTTTTACAAGCTCCAATACAATGACACTA
||| | | | || ||||| | | ||||| ||| | | | | ||| | | | ||| || | | |||| |||||||||||||| |||||||||||||| ||||| | || || || |||| || || || ||||||||||| | || |||| ||| ||
gttccagttccttcctctttcactcatgtgcagccatataattcatttagctataaagtgctcacagtatgtagtacaaagtcctgtttgtagtgtattcttgttgccacccacgaaaaat-gcggtggtcatgatcatatatactggtttcaaatttgg---acagGCCGTATACCACATGCCTACAACTGAGAATGACGCACCATCTAGCAGCATTCCCCTGGCACTTCAGAGCTTGTTTTACAAAATGCAGTACAGTGATACCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgggttctcattgaatccttgaccggacaactgaattttgcatgttgcttgtagGCTGTATACCACATGCCAACAACTGAGAATGATGCACCCACAGCAAGTATACCGTTGGCTCTCCAAAGTTTGTTTTACAAGCTCCAATACAATGACACTA
ccttgac putative branch site (score: 4)
tgaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatatattcttgttttttccttcagtttgttaaattccatgggttctcattgaatccttgaccggacaactgaattttgcatgttgcttgtagGCTGTATACCACATGCCAACAACTGAGAATGATGCACCCACAGCAAGTATACCGTTGGCTCTCCAAAGTTTGTTTTACAAGCTCCAATACAATGACACTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT