Sequence
atgc intronic sequence ATGC exonic sequencegtaggacactgcgaactgtgtcaatgctggtttctttctttgtatgtgaaaaatttcatggatactgaactacatatcggtgtttcagGTTGCCCCATATTGTGCTTCAAAGTGGGCAATTGAAGGTTTAACACGCTCCTTAGCAAAGGAGCTGCCTCCTGGATTGGCAGCAATTGCCCTTAGCCCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g35170.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g35170.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G128146_T01 (Zea mays), 3'ss of exon 3
-----gtaggacactgcgaactgtgtcaatgctggtttctttctttgtatgtgaaaaatttcatggatactgaactacatatcggtgtttcagGTTGCCCCATATTGTGCTTCAAAGTGGGCAATTGAAGGTTTAACACGCTCCTTAGCAAAGGAGCTGCCTCCTGGATTGGCAGCAATTGCCCTTAGCCCTG
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gtcatacagaaaaccatcaaatgcattatagttg-tttctttctgatgaatcaaaatcctcaatgcatactaaattgcacattgtcatttcagGTTGCTCCATATTGTGCTTCGAAGTGGGCGATTGAGGGCTTGACACGCTCGTTAGCTAAAGAGCTACCTCCTGGATTGGCAGCCATTGCTCTTAGCCCTG
upper sequence: LOC_Os02g35170.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G018037_T01 (Zea mays), 3'ss of exon 1
-----gtaggacactgcgaactgtgtcaatgctggtttctttctttgtatgtgaaaaatttcatggatactgaactacatatcggtgtttcagGTTGCCCCATATTGTGCTTCAAAGTGGGCAATTGAAGGTTTAACACGCTCCTTAGCAAAGGAGCTGCCTCCTGGATTGGCAGCAATTGCCCTTAGCCCTG
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gtcatacagaaaaccatcaaatgcattatagttg-tttctttctgatgaatcaaaatcctcaatgcatactaaattgcacattgtcatttcagGTTGCTCCATATTGTGCTTCGAAGTGGGCGATTGAGGGCTTGACACGCTCGTTGGCTAAAGAGCTACCACCTGGATTGGCAGCCATTGCTCTTAGCCCTG
upper sequence: LOC_Os02g35170.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G059361_T01 (Zea mays), 3'ss of exon 2
-----gtaggacactgcgaactgtgtcaatgctggtttctttctttgtatgtgaaaaatttcatggatactgaactacatatcggtgtttcagGTTGCCCCATATTGTGCTTCAAAGTGGGCAATTGAAGGTTTAACACGCTCCTTAGCAAAGGAGCTGCCTCCTGGATTGGCAGCAATTGCCCTTAGCCCTG
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gtcatacagaaaaccatcaaatgcattatagttg-tttctttctgatgaatcaaaatcctcaatgcatactaaattgcacattgtcatttcagGTTGCTCCATATTGTGCTTCGAAGTGGGCGATTGAGGGCTTGACACGCTCGTTGGCTAAAGAGCTACCTCCTGGATTGGCAGCCATTGCTCTTAGCCCTG
upper sequence: LOC_Os02g35170.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0035g01780.t01 (Vitis vinifera), 3'ss of exon 3
gtaggacactgcgaactgtgtcaatgctggtttctttctttgtatgtgaaaaatttcatggatactgaact-----------acatatcggtgtttca---gGTTGCCCCATATTGTGCTTCAAAGTGGGCAATTGAAGGTTTAACACGCTCCTTAGCAAAGGAGCTGCCTCCTGGATTGGCAGCAATTGCCCTTAGCCCTG
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--agggtactacgtctttcgatgaccttattttattccttttcagtctatgcttcatgttgacatttggctcactttctgaaacctaataatgtttcaacagGTTGCGCCTTATTGTGCTTCAAAATGGGCAGTTGAGGGTTTATCTAGATCAGTGGCAAAGGAGTTGCCCAGTGGACTTGCAATTGTTGCGCTTAATCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctttgtatgtgaaaaatttcatggatactgaactacatatcggtgtttcagGTTGCCCCATATTGTGCTTCAAAGTGGGCAATTGAAGGTTTAACACGCTCCTTAGCAAAGGAGCTGCCTCCTGGATTGGCAGCAATTGCCCTTAGCCCTG
tatgtgaaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggacactgcgaactgtgtcaatgctggtttctttctttgtatgtgaaaaatttcatggatactgaactacatatcggtgtttcagGTTGCCCCATATTGTGCTTCAAAGTGGGCAATTGAAGGTTTAACACGCTCCTTAGCAAAGGAGCTGCCTCCTGGATTGGCAGCAATTGCCCTTAGCCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC