Sequence
atgc intronic sequence ATGC exonic sequencegtacacaacattttctaacttatcagtagagtttattcttaagcaaatgacttaattatgtgattttttttcagGTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTTACTAAGATGACTTATGCCCAGGTTGCAGTATATGGCTTCAGCGAAAAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62500.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G07510.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------------------gtacacaacattttctaacttatcagtagagtttattcttaagcaaatgacttaattatgtgattttttttcagGTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTTACTAAGATGACTTATGCCCAGGTTGCAGTATATGGCTTCAGCGAAAAGG
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agaagtcaagaactcattaaggtttcaggtcataaactttctgttatttgttgttgaagatgtgaatcctgttaat--ttttctggtgggttttgattgcagGTATTGATTGGAAGAATATCCACTGGGGCTCAGAACGATCTGGAAAAGGTGACTAAGATGACTTATGCGCAAGTGGCAGTGTACGGATTCAGCGACAAGA
upper sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 7
------------------------gtacacaacattttctaacttatcagtagagtttattc-ttaagcaaatgacttaatt-atgtgattttttttcagGTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTTACTAAGATGACTTATGCCCAGGTTGCAGTATATGGCTTCAGCGAAAAGG
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atatttgcttacaatattagaaaagaaaagacgaacctctagtgttttgtttcagtgtttccgccgtgatgatgacagggttcatttcctatggatgcagGTTTTGATTGGTAGAATATCGACAGGAGCCCAAAATGATCTGGAGAAGGTAACAAAGATGACATATGCTCAGGTCGCAGTCTATGGTTTTAGTGACAAGG
upper sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------------------------------------------------------------gtacacaacattttctaac--ttatcagtagagtttattcttaagcaaatgacttaattatgtgatttttttt-----cagGTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTTACTAAGATGACTTATGCCCAGGTTGCAGTATATGGCTTCAGCGAAAAGG
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gtatagcacgtgtttttttgtctttgtcttgggtacgccctcttgaaaagatgcttaacaagatgcagaattgtttagactgtcagtatacttgcaatatacttgcaatcatgagaaaatggaagtcttgctgatcgttagagaagcagttttagttaatgttgatttttttactgttggttcgttgctttacacagGTACTGTTAGGTAAAATATCAACAGGTGCACAGAATGACTTGGAGAAAGTTACGAAAATGACTTATGCACAAGTTGCAGTATATGGGTTTAGTGAAAAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|58606880|gb|CK034913.1|CK034913EST: AGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAG GTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTT
genomic: AGCTTTTTGACATGACCTGCATGACACTAGGTGGCCGAGCTGCTGAGGAGgtacacaaca ... tttttttcagGTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcagtagagtttattcttaagcaaatgacttaattatgtgattttttttcagGTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTTACTAAGATGACTTATGCCCAGGTTGCAGTATATGGCTTCAGCGAAAAGG
acttaat putative branch site (score: 4)
ttttttttc putative PPT
aaatgacttaattatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacaacattttctaacttatcagtagagtttattcttaagcaaatgacttaattatgtgattttttttcagGTCTTGATTGGAAAGATCTCGACTGGTGCACAGAATGATCTGGAGAAAGTTACTAAGATGACTTATGCCCAGGTTGCAGTATATGGCTTCAGCGAAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG