Sequence
atgc intronic sequence ATGC exonic sequencegtatgctcacttttgacaaagtcaattatcacattcatattattggagacctggttatcatttattttatacatatattcagtataattgtatgctcatattgaggctatcttctgttctcgttttgctaatttgcagGGGAGTGAAGACATCTGACTCTGCTGCTGATATCAAAAAGGCATACCGCAAAGCAGCTCTTAGACATCACCCAGACAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G41520.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G41520.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g16680.1 (Oryza sativa), 3'ss of exon 4
gtatgctcacttttgacaaagtcaattatcacattcatattattggagacctggttatcatttattttatacatatattcagtataattgtatgctcatattgaggctatcttctgttctcgttttgctaatttgcagGGGAGTGAAGACATCTGACTCTGCTGCTGATATCAAAAAGGCATACCGCAAAGCAGCTCTTAGACATCACCCAGACAAA
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------------------------------------atgtttagaagaaattaattctgtatgagtttgttc-tgaaagaaaccttctcctctactgaaattc-gttggaagtaaatttacaccttttttgcatgcagAGGAATCGAACCATCTTGCACTTTCTTGGATATAAAGAAGGCATACCGCAAAGCAGCACTAAGGCATCATCCAGACAAA
upper sequence: AT2G41520.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G348697_T02 (Zea mays), 3'ss of exon 8
gtatgctcacttttgacaaagtcaattatcacattcatattattggagacctggttatcatttattttatacatatattcagtataattgtatgctcatattgaggctatcttctgttctcgttttgctaatttg---cagGGGAGTGAAGACATCTGACTCTGCTGCTGATATCAAAAAGGCATACCGCAAAGCAGCTCTTAGACATCACCCAGACAAA
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---------------------------------ctcttagtttctgatg---aattatc-ctgatgtgaggcagat-tctattttccgggtat---tatgtggagataaacttaattactaattatccttttctgtatcagGGGAGTGGAGCCATCCTGCTCTTCAGAAGATATTAAGAAGGCATACCGGAAAGCAGCATTGAGACATCACCCAGACAAG
upper sequence: AT2G41520.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv00s0252g00060.t01 (Vitis vinifera), 3'ss of exon 8
gtatgctcacttttgacaaagtcaattatcacattcatattattggagacct--ggttatcatttattttatacatatattcagtataattgtatgctcatattgaggctatcttctgttctcgttttgctaatttgcagGGGAGTGAAGACATCTGACTCTGCTGCTGATATCAAAAAGGCATACCGCAAAGCAGCTCTTAGACATCACCCAGACAAA
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---------------------------atgttgcccataggattgaaggcttttgagtctcattcagcttcctgaca----ccatgtttctgcaagcttcta--------attcagtatctcaaattttataatgc-cagGGGAATTAAACCATCTGAGACAGCAGCTGATATCAAGAAGGCATACCGGAAAGCTGCACTTAGACATCATCCAGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataattgtatgctcatattgaggctatcttctgttctcgttttgctaatttgcagGGGAGTGAAGACATCTGACTCTGCTGCTGATATCAAAAAGGCATACCGCAAAGCAGCTCTTAGACATCACCCAGACAAA
tgctaat putative branch site (score: 2)
ttttgct CT-rich tract
taattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctcacttttgacaaagtcaattatcacattcatattattggagacctggttatcatttattttatacatatattcagtataattgtatgctcatattgaggctatcttctgttctcgttttgctaatttgcagGGGAGTGAAGACATCTGACTCTGCTGCTGATATCAAAAAGGCATACCGCAAAGCAGCTCTTAGACATCACCCAGACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC