Sequence
atgc intronic sequence ATGC exonic sequence...cctggaaaaatgttcatattattgtaatcccatcaatattgttagataaggctttgatttacatatgttgtttatgctttatatgtttttttttattcagAATCGTTCACCAAGCATTTTGAGAAATATGGAGCTATATCTGATTCTGTGATCATGAAAGACAAGCATACAAAGATGCCTCGTGGATTTGGTTTTGTTAC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g37000.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g37000.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G104481_T02 (Zea mays), 3'ss of exon 1
cctggaaaaatgttcatattattgtaatcccatcaatattgttagataaggct-ttgatttacatatgttgtttatgctttatatgtttttttttattcagAATCGTTCACCAAGCATTTTGAGAAATATGGAGCTATATCTGATTCTGTGATCATGAAAGACAAGCATACAAAGATGCCTCGTGGATTTGGTTTTGTTAC
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---------atggagctataactg--attctgtgatcat-gaaggacaagcatactaggatgcct-cgtggatttggatttgt-tacattttccgatccgtctgtgcttgacagGGTTCTAGAGGATGAACATGTCATAGATGGAAGGACG--------------------------------------------------
upper sequence: LOC_Os06g37000.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G104481_T01 (Zea mays), 3'ss of exon 2
cctggaaaaatgttcatattattgtaatcccatcaatatt-gttagataaggct---ttgatttacatatgttgtttatgctttat---atgtttttttt---tattcagAATCGTTCACCAAGCATTTTGAGAAATATGGAGCTATATCTGATTCTGTGATCATGAAAGACAAGCATACAAAGATGCCTCGTGGATTTGGTTTTGTTAC
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----------gattgctgatctcatagagcaataagtttttgttagattagattgtgttaacttgtttatttcactcatcttttgttacatgcaccatttgcatgagcagAAACATTCACAAAGCATTTTCAGAAGTATGGAGCTATAACTGATTCTGTGATCATGAAGGACAAGCATACTAGGATGCCTCGTGGATTTGGATTTGTTAC
upper sequence: LOC_Os06g37000.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G064518_T01 (Zea mays), 3'ss of exon 2
cctggaaaaatgttcatattattgtaatcccatcaatattgttagataaggctttgatttacatatgttgtttatgctt---tatatgtttttttt---tattcagAATCGTTCACCAAGCATTTTGAGAAATATGGAGCTATATCTGATTCTGTGATCATGAAAGACAAGCATACAAAGATGCCTCGTGGATTTGGTTTTGTTAC
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--atatagattgctgatctcat-gtagcaata-catttttgttg--tactgtgataacttttttattttgcttatctttcgttatatgttccatttgcatgtgcagAAACATTCACAAAGCATTTTCAGAAGTATGGAGCTATAACTGATTCTGTGATCATGAAGGACAAGCATACTAGGATGCCTCGCGGATTTGGATTTGTTAC
upper sequence: LOC_Os06g37000.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G104481_T03 (Zea mays), 3'ss of exon 2
cctggaaaaatgttcatattattgtaatcccatcaatattgttagataaggctttgatttacatatgttgtttatgctttatatgtttttttttattcagAATCGTTCACCAAGCATTTTGAGAAATATGGAGCTATATCTGATTCTGTGATCATGAAAGACAAGCATACAAAGATGCCTCGTGGATTTGGTTTTGTTAC-----------------------------------------------------------
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----------------------------------------------------------tttcactcatcttttgttacatgcac-catttgcatgagcagaaacattcacaaagcattttcagaagtatggagctataactgattctgtgatcatgaagGACAAGCATACTAGGATGCCTCGTGGATTTGGATTTGTTACATTTTCCGATCCGTCTGTGCTTGACAGGGTTCTAGAGGATGAACATGTCATAGATGGAAMapped 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|11172404|gb|AU164268.1|AU164268EST: GTTTGCTCTCGCCGCCCACCACTTCCTCCTCCTCCTCCGACGAAGCTCCG AATCGTTCACCAAGCATTTTGAGAAATATGGAGCTATATCTGATTCTGTGA
genomic: GTTTGCTCTCGCCG-CCACCACTTCCTCCTCCTCCTCCGACGAAGCTCCGgttagctcgg ... ttttattcagAATCGTTCACCAAGCATTTTGAGAAATATGGAGCTATATCTGATTCTGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaggctttgatttacatatgttgtttatgctttatatgtttttttttattcagAATCGTTCACCAAGCATTTTGAGAAATATGGAGCTATATCTGATTCTGTGATCATGAAAGACAAGCATACAAAGATGCCTCGTGGATTTGGTTTTGTTAC
ctttgat putative branch site (score: 5)
tgtttttttttattc putative PPT
atatgttgtttatgct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctggaaaaatgttcatattattgtaatcccatcaatattgttagataaggctttgatttacatatgttgtttatgctttatatgtttttttttattcagAATCGTTCACCAAGCATTTTGAGAAATATGGAGCTATATCTGATTCTGTGATCATGAAAGACAAGCATACAAAGATGCCTCGTGGATTTGGTTTTGTTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG