Sequence
atgc intronic sequence ATGC exonic sequence...ttttccatcacttcagtgttccctgtataatattgctggctgcatcacatctcttattacttaattttcctcttcatctttacagaagtttgtggttaagGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g53060.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152775_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------ttttccatcacttcag--tgttccctgtataatattgctggc----tgcatcacatctctta--ttacttaattttcctct-----tcatctttacagaagtttgtggttaagGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT-------------------------
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gtatgtctccaagttccttcttacttggatcttggcaatgagatattctctctagcatattagtatgactgaaggttattagttgtgtaataaaacgaatagagtacaacactagccccaattttcctaatatgtttctaatgttcatatatgcagAAATTTGTGGTGAAGGTAGTTTCCCTTGCTATGGCCCGTGATGGTGCTAGTGGAGGGGTTGTCCGTACAGTTACAGTAAGTTCTCTCTCTATTTTTTATG
upper sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 6
----------------------------------------------------------ttttccatcacttcag--tgttccctgtataatattgctggc----tgcatcacatctctta--ttacttaattttcctct-----tcatctttacagaagtttgtggttaagGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT
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gtatgtctccaagttccttcttacttggatcttggcaatgagatattctctctagcatattagtatgactgaaggttattagttgtgtaataaaacgaatagagtacaacactagccccaattttcctaatatgtttctaatgttcatatatgcagAAATTTGTGGTGAAGGTAGTTTCCCTTGCTATGGCCCGTGATGGTGCTAGTGGAGGGGTTGTCCGTACAGTTACA
upper sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 6
ttttccatcacttcag--tgttccctgtataat--------attgctggctgcatcacatctctta--ttacttaattttcctct-----tcatctttacagaagtttgtggttaagGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT
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--tagtatgactgaaggttattaattgtgtaaagcgaatagactatagagtacaaaacttgcctcaattttcctaatatgtttctaatggtcatatatacagAAATTTGTGGTGAAGGTAGTTTCCCTTGCTATGGCCCGTGATGGTGCTAGCGGAGGGGTTGTCCGTACAGTTACAMapped 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|163920296|gb|EG710592.1|EG710592EST: CTCTGGATCTGCTGCTGATACACAA GTAATTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGT
genomic: CTCTGGATCTGCTGCTGATACACAAgtaatttccg ... tgtggttaagGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacatctcttattacttaattttcctcttcatctttacagaagtttgtggttaagGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT
acttaat putative branch site (score: 4)
tcttattacttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttccatcacttcagtgttccctgtataatattgctggctgcatcacatctcttattacttaattttcctcttcatctttacagaagtttgtggttaagGTAGTTTCCCTTGCTATAGCCCGTGATGGTGCTAGTGGAGGGGTTGTTCGTACCGTCACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - ccctgta
- - - - - - - - - - - - - - - - -tgctggc
- - - - - - - - - - - - - - - - - - - - tgcatca