Sequence
atgc intronic sequence ATGC exonic sequencegtaattcacatatatttcaaattttgttgcctattagtttggtttctatgttactccatgcataatatgtgccctgttccacttcagCGTGAAAATTTCCAGATGGAGGGACCAACAGGAGTTATGAAGCAGTTGCAAGCATTGTGGAAGATCATGGAAATAACTGATGTAGAATTATTTGAACATT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01010.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01010.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G031043_T01 (Zea mays), 3'ss of exon 8
gtaattcac-----atatatttcaaattttgttgcctattagtttggtttctatgttact-----ccatgcataatatgtgcc-ctgttccacttcagCGTGAAAATTTCCAGATGGAGGGACCAACAGGAGTTATGAAGCAGTTGCAAGCATTGTGGAAGATCATGGAAATAACTGATGTAGAATTATTTGAACATT
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gtaatttgcctctgacataaattacagtacaatgtccatttatttggcatttacattaataatcatgatgaataatgtaaatctctgctgctcctcagCGTGAAAATTTCCAGATGGAGGGACCAACAGGAGTTATGAAGCAATTGCAAGCATTGTGGAAGATAATGGAACTGACAGATGCTGAATTATTTGAACATT
upper sequence: LOC_Os01g01010.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G59570.1 (Arabidopsis thaliana), 3'ss of exon 7
------------------gtaattcacatatatttcaaattttgttgcctattagttt-----ggtttctatgttactccatgcataatatgtgccctgtt-ccacttcagCGTGAAAATTTCCAGATGGAGGGACCAACAGGAGTTATGAAGCAGTTGCAAGCATTGTGGAAGATCATGGAAATAACTGATGTAGAATTATTTGAACATT
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gtattccaatgcttactgatacgtaacatgtgttttagttttcccctaccagcaagtgacaaaggctgtggtgtaatatgatgttcttttgctatgtggttattactgtagCGTGCTAATTTCCAGATGGAGGGACCAACTGGAGTAATGGATCAATTGCAATCACTATGGCGTATATTGCAACTCACAGATAAAGAAATGTTTTCACACC
upper sequence: LOC_Os01g01010.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv00s0226g00160.t01 (Vitis vinifera), 3'ss of exon 7
gtaattcacatatatttcaaattttgttgcctattagtttggtttctatgttactccatgcataatatgtgccctgttccacttcagCGTGAAAATTTCCAGATGGAGGGACCAACAGGAGTTATGAAGCAGTTGCAAGCATTGTGGAAGATCATGGAAATAACTGATGTAGAATTATTTGAACATT
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gtatccctaaaattgtctagtatgttcagaaaattaatttgattt-tatttcact------aacattcatattccaaatttctccagTGTGAAAATTTTCAGATGGAAGGACCAACTGGAGTGATGAAAAAGTTGCAAGCATTGAAGCATATTTTGGAGCTCACTGACAGGGAAATGTTTGCACACT
upper sequence: LOC_Os01g01010.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv00s0226g00020.t01 (Vitis vinifera), 3'ss of exon 3
gtaattcacatatatttcaaattttgttgcctattagtttggtttctatgttactccatgcata-atatgtgccctgttccacttcagCGTGAAAATTTCCAGATGGAGGGACCAACAGGAGTTATGAAGCAGTTGCAAGCATTGTGGAAGATCATGGAAATAACTGATGTAGAATTATTTGAACATT
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gtatttc-taaatttggctaatatgtttggaaaaacatatatttttttctttcactaatgtatatatatatatttcacacttctccagCGTGAAAATTTTCAGATGGAAGGGCCAACTGGAGTGATGAAGCAGTTGCAAGCATTATGGCATATTTTGGAACTCACTGACAGGGAAATGTTTGGACACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagtttggtttctatgttactccatgcataatatgtgccctgttccacttcagCGTGAAAATTTCCAGATGGAGGGACCAACAGGAGTTATGAAGCAGTTGCAAGCATTGTGGAAGATCATGGAAATAACTGATGTAGAATTATTTGAACATT
ccctgttccacttc CT-rich tract
ataatatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcacatatatttcaaattttgttgcctattagtttggtttctatgttactccatgcataatatgtgccctgttccacttcagCGTGAAAATTTCCAGATGGAGGGACCAACAGGAGTTATGAAGCAGTTGCAAGCATTGTGGAAGATCATGGAAATAACTGATGTAGAATTATTTGAACATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA