Sequence
atgc intronic sequence ATGC exonic sequence...aatatattatgctcttgttttcctatttgtttgctgattcaacatcttgagttatatttgatgcaacaatgatgtttgatctgttatgatttctttgcagGAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCCAGGATGTTGCTGGTGATGTTCGAATGACTGATAGTCGTTCAGATGAAGC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g53900.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AC203173.3_FGT004 (Zea mays), 3'ss of exon 1
aatatattatgctcttgttttcctatttgtttgctgattcaacatcttgagttatat-ttgatgcaaca-atgatgtttgatctgttatgatttctttgcagGAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCCAGGATGTTGCTGGTGATGTTCGAATGACTGATAGTCGTTCAGATGAAGC
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--tttgattggtcatctgtttctaatgtgctcctctatgatgcatgtccacttggatgttgaagttttgcatcattcattatgtattattgtttttttgcagGCAAGTCTACACTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACTCGTGCAGATGAAGC
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G040369_T01 (Zea mays), 3'ss of exon 2
aatatattatgctcttgttttcctatttgt-ttgctgattcaacatcttgagttatatttgatgcaacaatgatgtttgat-ctgttatgatttctttgcagGAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCCAGGATGTTGCTGGTGATGTTCGAATGACTGATAGTCGTTCAGATGAAGC
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-ctttaatgctctatgacgcacatgttgaagttgctggtgatgttctctaggcttatctttttgtcatcttg-tacctgatgctattattacttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACTCGGGCAGATGAAGC
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G095851_T01 (Zea mays), 3'ss of exon 2
aatatattatgctcttgttttcctatttgt-ttgctgattcaacatcttgagttatatttgatgcaacaatgatgtttgat-ctgttatgatttctttgcagGAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCCAGGATGTTGCTGGTGATGTTCGAATGACTGATAGTCGTTCAGATGAAGC
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-ctttaatgctctatgacacacatgttgaagttgctggtgatgttctctaggcttatccttttgtcatcttg-tacctgatgctattattacttctttgcagGCAAGTCTACGCTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGTGATGTTCGCATGACTGATACTCGGGCAGATGAAGC
upper sequence: LOC_Os01g53900.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G113250_T01 (Zea mays), 3'ss of exon 2
aatatattatgctcttgttt--tcctatttgtttgctgattcaacat-cttgagttatatttgatgcaacaatgatgtttgat-ctgttatgatttctttgcagGAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCCAGGATGTTGCTGGTGATGTTCGAATGACTGATAGTCGTTCAGATGAAGC
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aacttttgatttggttgtctgttcctaatgttgtactagtcaatgatgcacatgttgaagtt----ccacactgtttttatatgctactattaattctttgcagGCAAGTCTACACTTACAGATTCCCTTGTGGCAGCTGCTGGGATTATTGCCCAGGAAGTTGCTGGCGATGTTCGCATGACTGATACTCGTGCAGATGAAGCMapped 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|86888335|gb|CI303617.1|CI303617EST: CAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATG GAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCC
genomic: CAAGAAGCATAACATCCGTAACATGTCTGTTGTCGCTCATGTGGACCATGgtatgtttga ... ttctttgcagGAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgagttatatttgatgcaacaatgatgtttgatctgttatgatttctttgcagGAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCCAGGATGTTGCTGGTGATGTTCGAATGACTGATAGTCGTTCAGATGAAGC
gtttgat putative branch site (score: 5)
tttctttgc putative PPT
ttatatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatatattatgctcttgttttcctatttgtttgctgattcaacatcttgagttatatttgatgcaacaatgatgtttgatctgttatgatttctttgcagGAAAATCTACCCTTACTGATTCCCTTGTGGCAGCTGCTGGAATTATAGCCCAGGATGTTGCTGGTGATGTTCGAATGACTGATAGTCGTTCAGATGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - ttatgct
- - - - - - - - - - - - - - - -tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttatgat