Sequence
atgc intronic sequence ATGC exonic sequence...gtgtatttggatagtttaatattttctgttcaatttaagcatcagtacatagctatgctatatcacaatgacttgacgttatgcgggagaaacatttcagGAATCCGGATCATGACGAGGACACAGAAAAGCCACCCCTTAGACCCACTATCTGCTGCTGAAATTTCTGTGGCTGTAGCAACTGTCAGAGCTTCTGGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g38010.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 1
gtgtatttggatagtttaatattttctgttcaatttaagcatcagtacatagctatgctatatcacaatgacttgacgttatgcgggagaaacatttc---------agGAATCCGGATCATGACGAGGACACAGAAAAGCCACCCCTTAGACCCACTATCTGCTGCTGAAATTTCTGTGGCTGTAGCAACTGTCAGAGCTTCTGGAAG-
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-catatctgtttttcttatcatctt-tgcctagttta----tctgctcat--ctctcctttatgaaattgcttttcca--aagttgaagaactgttctttttggcataggTATCACTGTCATGGTGAGAGCTCAAACCAGCCACCCCTTGGATCCACTAACTGCTGCTGAAATATCAGTAGCTGTAGCGACCGTTCGAGCAGCTGGAGCA
upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 1
-----gtgtatttggatagtttaatattttctgttcaatttaagcatcagtacatagctatgctatatcacaatgacttgacgttatgcggga-gaaacatttcagGAATCCGGATCATGACGAGGACACAGAAAAGCCACCCCTTAGACCCACTATCTGCTGCTGAAATTTCTGTGGCTGTAGCAACTGTCAGAGCTTCTGGAAG
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caattttttatttgca-agttcttgaatgcaggctttgctt--gttttcatgttttttaatattagctaactgtgtttctatttttgttgtaatgttgcatagGAGTCGTTGCTGCAATGCCAAGGGCACAGTCAAGCCACCCTTTGGATCCTTTATCTGCTGCTGAAATCTCTGTGGCTGTGGCAACTGTGCGGGCTGCTGG---
upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 1
gtgtatttggatagtttaatattttctgttcaatt-taagcatc-agtacatag--ctatgctatatcac-aatgacttgacgttatgcgggagaaacatttcagGAATCCGGATCATGACGAGGACACAGAAAAGCCACCCCTTAGACCCACTATCTGCTGCTGAAATTTCTGTGGCTGTAGCAACTGTCAGAGCTTCTGGAAG
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----ggttgactggcctttccctttctgcactgttgcagatattgaatagtttgtgctcttttgcattgttgatgaattggttttgt-tgctatgctttttgcagGGATCCAGATCATGACAAGGGCTCAAACCTGCCATCCGTTGGACCCATTATCTGCAACTGAAATCTCAGTGGCTGTGGCAACTGTCAGAGCTGCTGGAGC
upper sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 1
gtgtatttggatagtttaatattttctgttcaatttaagcatcagtacatagctatgct---atatcacaatgacttgacgttatgcgggagaaacatttcagGAATCCGGATCATGACGAGGACACAGAAAAGCCACCCCTTAGACCCACTATCTGCTGCTGAAATTTCTGTGGCTGTAGCAACTGTCAGAGCTTCTGGAAG
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---ttcattgttaaattgctactactctaaccacttaagtgtttataggtcgaatggcatcaatgtcatatggcttatttattttgtttctttgcttgtgtagGGATTCCAATCATGTTGAGAGCTCAGACCAGCCACCCTTTGGACCCTTTATCCGCTGCTGAAATCTCAGTGGCAGTGGCAACTGTCAGAGCAGCTGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatagctatgctatatcacaatgacttgacgttatgcgggagaaacatttcagGAATCCGGATCATGACGAGGACACAGAAAAGCCACCCCTTAGACCCACTATCTGCTGCTGAAATTTCTGTGGCTGTAGCAACTGTCAGAGCTTCTGGAAG
acttgac putative branch site (score: 4)
aaacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtatttggatagtttaatattttctgttcaatttaagcatcagtacatagctatgctatatcacaatgacttgacgttatgcgggagaaacatttcagGAATCCGGATCATGACGAGGACACAGAAAAGCCACCCCTTAGACCCACTATCTGCTGCTGAAATTTCTGTGGCTGTAGCAACTGTCAGAGCTTCTGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - -ttctgtt
- - - - - - - - - - - - - - - - - - - gcatcag
- - - - - - - - - - - - - - - - - - - - - - - - - -gctatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacttg