Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgattgtaaaatctatggaagttcattttatttctcatgtgtactactgcgtgtacacctttttatattttgtatgcgcatataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC
Basic information
species | Oryza sativa |
transcript | LOC_Os08g08200.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g08200.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G042398_T01 (Zea mays), 3'ss of exon 11
gtaagttgattgtaaaatctatggaagttcattttatttctcatgtgtactactgcgtgtacacctttttatattttgtatgcgcatataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC
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----------------------------------------------gtactggaggggttctattgcttcaacagtcctctgtgcagcctatatgcctcaccaatgcttgt--tacatattgtttgccaatgtttcacagTATGATCTCGAGCTGGTTCTGATGAAGAACTTCCATGAATTTGTACACGAGTACTTGCAAAAACCAGAGTTCGCCGAGCTGATGCGGAGGCTGGGTGCCC
upper sequence: LOC_Os08g08200.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 10
gtaagttgattgtaaaatctatggaagttcattttatttctcatgtgtactactgcgtgtacacctttttatattttgtatgcgcatataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC
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-----------------------------caaaatgtttttc-----cacttttacatctcaatcatctcatacctttttaa--tatgggctgtttaactttgaggcat-tagtgagtttgtgtttggctt---ttgcagTATGATTTGGATCTGGTTTTAGTGAAGAACTCACATGAATTTGTGGATGAGTACTTGAAAAAACCAGAATTTGTTGAGCTTATGCGGAGGCTAGGTGCTTMapped 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|66916049|gb|CX102897.1|CX102897EST: TTTCTTAAACTATTGCGAGTAACACTCTGCTGGTTTTCC-TTATTTTGCA TATGACCTGGAGTT
genomic: TTCCTTAAACTATTGCGAGTAACACTCTGCTG-TTTTCCCTTATTTTGCAgtaagttgat ... tgtattgcagTATGACCTGGAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC
ttctgac putative branch site (score: 2)
ttttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgattgtaaaatctatggaagttcattttatttctcatgtgtactactgcgtgtacacctttttatattttgtatgcgcatataaagttgcaatcagatgcatgtagttctgacacgttttgaatgtattgcagTATGACCTGGAGTTGGTTCTGACGAAAAACTTCCATGAATTTGTACACGAGTACTTGCAAAAGCCAGAGTTTGCTGAGCTCATGCGGAGGCTGGGTGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA