Sequence
atgc intronic sequence ATGC exonic sequence...tttcaatgtgcactttttgtctttgtactctatgttttggtggttataatctagattataatagctaggagctatgtactgaacctgattttgttcttagGAAAACCGTCTGCGTCAAGAAATAGAAGATCTTGAGAAAGATACAGGATACAAGTTGAGAGTTCTTGCACAAAATTATCCTGATACACCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g34950.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g34950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G022876_T01 (Zea mays), 3'ss of exon 2
tttcaatgtgcactttttgtctttgtactctatgttttggtggttataatctagattataatagctaggagctatgtactgaacctgat-tttgttcttagGAAAACCGTCTGCGTCAAGAAATAGAAGATCTTGAGAAAGATACAGGATACAAGTTGAGAGTTCTTGCACAAAATTATCCTGATACACCAG
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-ggagaggaatactttcgttgattgctttttttgttctacctgagatgcactgtctcttgttagcaacacatcaatcatagaggaggttatttgttcttagGAAAACCGTTTGCGCCAAGAGATAGAAGACCTGGAGAAAGATACAGGGTACAAACTGCGAGTTCTTGCACAAAATTATCCTGATACACCTG
upper sequence: LOC_Os07g34950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G52970.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------tttcaatgtgcactttttgtctttgtactctatgttttg---gtggttataatctaga---ttataatagctaggagctatgtactgaacctgattttgttctt----------agGAAAACCGTCTGCGTCAAGAAATAGAAGATCTTGAGAAAGATACAGGATACAAGTTGAGAGTTCTTGCACAAAATTATCCTGATACACCAG
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gtatgcatgcttgtaccatccatctatttttgaggtttgattaaagcacttgtttcttgttaatgtcatgtggatctatt-tgcttattctgtagatttttagtgtatttctgattttgaatgttttcgccgcttttggttttcttttcttaatgatgttgttctttgagagttatagGAGAAGAGAATTGCTCAAGAAATCGCTAATCTTGAGAAAGATACAGGATTCAAGTTGAGAGTCTTGGCTCAAAACTATCCCGTTACCCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatctagattataatagctaggagctatgtactgaacctgattttgttcttagGAAAACCGTCTGCGTCAAGAAATAGAAGATCTTGAGAAAGATACAGGATACAAGTTGAGAGTTCTTGCACAAAATTATCCTGATACACCAG
acctgat putative branch site (score: 4)
ttttgttctt CT-rich tract
tagattataata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcaatgtgcactttttgtctttgtactctatgttttggtggttataatctagattataatagctaggagctatgtactgaacctgattttgttcttagGAAAACCGTCTGCGTCAAGAAATAGAAGATCTTGAGAAAGATACAGGATACAAGTTGAGAGTTCTTGCACAAAATTATCCTGATACACCAG
- - aatgtgc
- - - - - - - - - - - - - - -ctatgtt
- - - - - - - - - - - - - - - - - - -tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtactg