Sequence
atgc intronic sequence ATGC exonic sequencegtaatgttattgttgctttgcttgcttttagagcttgtcttttccaaacattgattgatcttctggttttggcagTCTAAAAACGCGTTGCTGTCAACGTTCTTGTTCCTAGATCAAATTGTGTGGCTTGGCAGGACTGGGATTTACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01820.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G029824_T03 (Zea mays), 3'ss of exon 2
----------------------------gtaatgtt-attgttgctttgcttgcttttagagcttgtcttttccaaacattgattgatcttctggttttg-----------gcagTCTAAAAACGCGTTGCTGTCAACGTTCTTGTTCCTAGATCAAATTGTGTGGCTTGGCAGGACTGGGATTTACAAG
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gtaaatcgacttctcccctccacacagtacactgttcatcaagaaatcccccccgtttaggaatcacagggttcgaa-acgaattaacctgcgggttcttcttctacgattgcagTCCAAAAACGCGCTGCTTTCGACGTTCTTGTTCTTGGATCAGTTTGTGTGGCTCGGACGAACGGGGATCGTCAAG
upper sequence: AT1G01820.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S3_624V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtaatgttattgttgctttgcttgctt------ttagag-------cttgtcttttcca--aacattgattgatcttct---------ggttttggcagTCTAAAAACGCGTTGCTGTCAACGTTCTTGTTCCTAGATCAAATTGTGTGGCTTGGCAGGACTGGGATTTACAAG
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caagttttttctgatacgaagtttgtttatagtattagaggcagtcactagttttttgcgttaataatgattgactttttttgcattgaaaattggtcagGCGAAAAATGCGTTGGTCGGAACCTTCTTGTTCCTTGATCAAATTGTGTGGGCTGGAAGAACTGGCATTTACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgcttttagagcttgtcttttccaaacattgattgatcttctggttttggcagTCTAAAAACGCGTTGCTGTCAACGTTCTTGTTCCTAGATCAAATTGTGTGGCTTGGCAGGACTGGGATTTACAAG
gattgat putative branch site (score: 4)
ttttaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgttattgttgctttgcttgcttttagagcttgtcttttccaaacattgattgatcttctggttttggcagTCTAAAAACGCGTTGCTGTCAACGTTCTTGTTCCTAGATCAAATTGTGTGGCTTGGCAGGACTGGGATTTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA