Sequence
atgc intronic sequence ATGC exonic sequencegtatgtacttaatacagtcatctttcatttgtaccagattattctctgctctttgagtttactgattattacctttcctactagTAATCTTAATGGCTGCTATGGCATACCAGCTGTCCACTACAAGGGTCGTCAGGGCGACTACTATATTCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g07560.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 1
gtatgtacttaatacagtcatctttcatttgtaccagattattctctgctctttgagtttactgattattaccttt-cctactagTAATCTTAATGGCTGCTATGGCATACCAGCTGTCCACTACAAGGGTCGTCAGGGCGACTACTATATTCTT
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gtatgttgctcatcctattgtctttcctttgtcatgggc--------actattt---ctttctgactattggcattgtttgctagCACTTTCAATGGTTGCTATGGCATACCATCGGTCCACTACAAGGGTCGTCAGGGCGAATACTATATACTT
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 4
gtatgtacttaatacagtcatctttcatttgtaccagattattctctgctctttgagtttactgattattaccttt-cctactagTAATCTTAATGGCTGCTATGGCATACCAGCTGTCCACTACAAGGGTCGTCAGGGCGACTACTATATTCTT
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gtatgttgctcatcctgccttcttttctttttgtggagactttcttt--------------ctgactattggtattgtttgctagCACTCTCAATGGTTGCTATGGCATACCATCGGTCCACTACAAGGGTCGTCAGGGCGACTACTATATACTT
upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 4
gtatgtacttaatacagtcatctttcatttgtaccagattattctctgctctttgagtttactgattattaccttt-cctactagTAATCTTAATGGCTGCTATGGCATACCAGCTGTCCACTACAAGGGTCGTCAGGGCGACTACTATATTCTT
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gtatgttgctcatcctgttgtctttcctttgtcgtgggc--------actattt---ctttctgactattggcattgtttgctagCACTCTCAATGGTTGCTATGGCATACCATCGGTCCACTACAAGGGTCGTCAGGGCGAATACTATATACTTMapped 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|66915500|gb|CX102348.1|CX102348EST: AACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCA TAATCTTAATGGCTGCTATGGCATACCAGCTGTCCACTACAAGGGTCGTCA
genomic: AACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCAgtatgtactt ... ttcctactagTAATCTTAATGGCTGCTATGGCATACCAGCTGTCCACTACAAGGGTCGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaccagattattctctgctctttgagtttactgattattacctttcctactagTAATCTTAATGGCTGCTATGGCATACCAGCTGTCCACTACAAGGGTCGTCAGGGCGACTACTATATTCTT
tactgat putative branch site (score: 2)
ttattacctttcct CT-rich tract
tttactgattatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtacttaatacagtcatctttcatttgtaccagattattctctgctctttgagtttactgattattacctttcctactagTAATCTTAATGGCTGCTATGGCATACCAGCTGTCCACTACAAGGGTCGTCAGGGCGACTACTATATTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG