Sequence
atgc intronic sequence ATGC exonic sequence...gccacgttggcaagtgaatatgtacatgagtctagttttctaggctctcatcaatatatggtagtatgcttagttatactcttttttttttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g43570.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G375904_T01 (Zea mays), 3'ss of exon 5
-gccacgttggcaagtgaatatgtacatgagtctagttttctaggctctcatcaatatatggtagtatgcttagttatactcttttttttttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG
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tgtctatcaagattccccccttttccataagcttccttcttgctgcgctgaggtacacttgagcaca-gttgacatgtttaatcgcaattttgggacacagGCATACTCAACAGTCGGTACACCTGATTATATTGCTCCAGAAGTGCTACTGAAGAAAGGATATGGAACGGAGTGTGACTG
upper sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G30640.1 (Arabidopsis thaliana), 3'ss of exon 6
gccacgttgg-caagtgaatatgtacatgagtctagttttctaggctctcatcaatatatggtagtatgcttagttatact-cttttttttttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG
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tttgcattaatctcctttggaagtttcctattttagttatttata-tgacctttccatataatcgga-gcgtaataagatggctctttcgtgtatcgatcagGCTTTTTCTACAGTAGGAACTCCCGATTACATTGCCCCTGAGGTGCTGCTGAAGAAAGGGTATGGAATGGAGTGTGATTG
upper sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 3'ss of exon 6
gccacgttggcaagtgaatatgt-acatgagtctagttttctaggctctcatcaatatatggtagtatgcttagttatactcttttttttttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG
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gccactctggactacacttcttttatttgaataaaaatctcaggtattggatatattttgagtctgttttgtatttatagt-tctgtcatatgctatctagGCTTATTCAACAGTTGGGACTCCCGACTACATTGCCCCAGAAGTACTGCTGAAGAAAGGATATGGAATGGAGTGTGATTG
upper sequence: LOC_Os05g43570.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------gccacgttggcaagt---gaatatgtacatgagtctagttttctaggctctcatcaatatatg-----gtagta------tgcttagttatactcttt--tttt---------tttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG
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gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgt-catagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactccattgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcatcaatatatggtagtatgcttagttatactcttttttttttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG
ttatactctttttttt CT-rich tract
ttagttatactctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccacgttggcaagtgaatatgtacatgagtctagttttctaggctctcatcaatatatggtagtatgcttagttatactcttttttttttggcatgcagGCATATTCAACGGTTGGTACTCCTGATTACATTGCTCCAGAGGTTCTGCTGAAGAAAGGATATGGAATGGAATGTGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA