Sequence
atgc intronic sequence ATGC exonic sequencegtaattgttttacttagttattatgatattgagctcatttctagttgagttggtcttgctgtcttggtctccaacaggcggtctctaaccagagtttcaccttttgtgttcagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGATATTGTTTTTACTCGCTCAACTCGTGGAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36270.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os10g10190.1 (Oryza sativa), 3'ss of exon 5
gtaattgttttacttagttattatgatattgagctcatttctagttgagttggtcttgctgtcttggtctccaacaggcggtctctaaccagagtttcaccttttgtgttcagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGATATTGTTTTTACTCGCTCAACTCGTGGAGG
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-------ttttttctaattatgtaggcactttatgcttttatgtgaaaaacaatttt------ttaatcaatgactgttggttattcattttgcacttttctccacaacacagATGGAAATGGCTTTAAGACAAGCACGATGAGACTTGGTGCTGATGCAATAGTGTTTACTCGCGCAAACCGTGGAAG
upper sequence: AT4G36270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G021864_T01 (Zea mays), 3'ss of exon 5
gtaattgttttacttagttattatgatattgagctcatttctagttgagttggtcttgctgtcttggtctccaacaggcggtctctaaccagagtttcaccttttg----tgttcagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGATATTGTTTTTACTCGCTCAACTCGTGGAGG
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--------tataattttttatt-tagtatctagcttctttataatagcat--gtataaaactcttggtatt------gctgtctcttgttactttcttaccttcttctactgcgcagATGGAAATGGCTTTAAGACAAGCACAATGAGACTTGGTGCAGATGCAATTGTTTTTACTCGTGCTATCCGAGGAGG
upper sequence: AT4G36270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 4
gtaattgttttacttagttattatgatattgagctcatttctagttgagttggtcttgctgtcttggtctccaacaggcggtctctaaccagagtttcaccttttgtgttcagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGATATTGTTTTTACTCGCTCAACTCGTGGAGG
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-----ttttcagatcaataaaatttctctctctctctctctctctgaaatttctctttctctcagaaattctt-----cactttccaagtaacat--catgttttat-tctagATGGCAATGGATTCAAGACTAGTACCATGAGACTGGGTGCTGATGTTATTGTTTTCAGTCGGGCAATGCATTCAGG
upper sequence: AT4G36270.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G05800.1 (Glycine max), 3'ss of exon 6
gtaattgttt-tacttagttattatgatattgagctcatttctagttgagttggtcttgctgtcttggtctccaacaggcggtctctaaccagagtttcaccttttgtgttcagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGATATTGTTTTTACTCGCTCAACTCGTGGAGG
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--aacagtacataagtgacttttatcatatt---ttcagat-taataaaatttctctttctctctgaaattctt-----cactttccaagtaacat--catgttttat-tctagATGGCAATGGTTTCAAAACTAGTACCATGAGATTGGGTGCTGATGTTATTGTTTTCAGTCGGGCAATGCATTCAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtcttggtctccaacaggcggtctctaaccagagtttcaccttttgtgttcagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGATATTGTTTTTACTCGCTCAACTCGTGGAGG
ctctaac putative branch site (score: 2)
tttcacctttt putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgttttacttagttattatgatattgagctcatttctagttgagttggtcttgctgtcttggtctccaacaggcggtctctaaccagagtttcaccttttgtgttcagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGATATTGTTTTTACTCGCTCAACTCGTGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG