Sequence
atgc intronic sequence ATGC exonic sequence...caaacttttaatgtatatatcccacagtacatatattgcagttaaagacatcctagcaatttgttaacttagccaatcaaaatcaactgtatcttctcagATCAGATAAGGCAGGAAAAATGCTTGCTGAAGTGCTTCTCAAGGGATTGCAAGGAAATAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02170.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G092776_T03 (Zea mays), 3'ss of exon 11
--------------------------------------------caaacttttaatgtatatatcccacagtacatatattgcagttaaagacatcctagcaatttgttaacttagccaatcaaaatcaactgtatcttctcagATCAGATAAGGCAGGAAAAATGCTTGCTGAAGTGCTTCTCAAGGGATTGCAAGGAAATAG
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gtaaatgcaaacccttgtagtacaatgtcttgtgtcaaactggcgaagtttccaatactaaaatttctctgtgctaatatactagttatctgtagtgtacctaacagcttgtttagcgaactga--tgaactgtatcctctcagATCAGATAAGGCAGGAAAAATGCTTGCAGAAGTGCTTCTTAAGGGACTGCAAGGAAACAG
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA01G37420.1 (Glycine max), 3'ss of exon 9
-caaacttttaatgtatatatcccacagtacatatattg-cagttaaagaca-tcctagcaatttgttaacttagccaatcaaaatcaactgtatcttctcagATCAGATAAGGCAGGAAAAATGCTTGCTGAAGTGCTTCTCAAGGGATTGCAAGGAAATAG
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ttactttattaaaaaaaacacttttttaacaatacaataattgttcaagtcagtttccatccttagtttgc--aattaatcctgcattatctca-cttttcagATCAGACAAGGCAGGAAAGTTGCTTGCTGAAGTATTATTGGGAGGGTTGCAGGGAAATAG
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA11G07870.1 (Glycine max), 3'ss of exon 8
--------caaacttttaatgtatatatcccacagtacatatattgcagttaaagacatcctagcaatttgttaacttagccaatcaaaatcaactgtatc-ttctcagATCAGATAAGGCAGGAAAAATGCTTGCTGAAGTGCTTCTCAAGGGATTGCAAGGAAATAG
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caaggaggcatgttttcaatttttgtcatctcaaggaaaaattt----gttacagtcagttt--ccattc-ttagtttg--caattaatcctgcttatctcactttcagATCAGACAAGGCAGGAAAGTTGCTTGCTGAAGTATTATTGGGAGGATTGCAGGGAAATCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agacatcctagcaatttgttaacttagccaatcaaaatcaactgtatcttctcagATCAGATAAGGCAGGAAAAATGCTTGCTGAAGTGCTTCTCAAGGGATTGCAAGGAAATAG
tgttaac putative branch site (score: 2)
tatcttctc putative PPT
aatttgttaactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaacttttaatgtatatatcccacagtacatatattgcagttaaagacatcctagcaatttgttaacttagccaatcaaaatcaactgtatcttctcagATCAGATAAGGCAGGAAAAATGCTTGCTGAAGTGCTTCTCAAGGGATTGCAAGGAAATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA