Sequence
atgc intronic sequence ATGC exonic sequence...agtgccaaataacaaaatcataaaaaatttcctagcagtgcattttgtcctgttgtgttttgatggtttcttactcctcccattacttttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.4 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 6
agtgccaaataacaaaatcataaaaaatttccta-gcagtgcattttgtcctgt-tgtgttttgatggtttcttactcc---tcccattacttt-tcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
| ||| | | | | || | | | | | | | | | || | |||| | | || || || | ||||||||||||||||||||||| ||||| || ||||||||| |||| || || ||||||||||| ||||||||||| |||| |||||||||||||||||| |||||||||
------atatacttagttttttgcactctttttctgtatttcgtccaacttcatgtagagtctgttctcttctggcctcagttcttgtttctctctcatatggcagTGTTGCTCATTTTTTGGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 17
agtgccaaataacaaaatca-taaaaaatttcctagcagtgcattttgtcctgt-tgtgttttgatggtttcttactcc---tcccattacttt-tcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
| ||| | | | | ||| | | | | | | | | || | |||| | | || || || | ||||||||||||||||||||||| ||||| || ||||||||| |||| || || ||||||||||| ||||||||||| |||| |||||||||||||||||| |||||||||
------atatacttagttttctgcactctttttctgtatttcgtccaacttcatgtagagtctgttctcttctagcctcagttcttgtttctctctcatatggcagTGTTGCTCATTTTTTGGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 16
agtgccaaataacaaaatcataaaaaatttcctagcagtgcattttgtcctgttgtgttttga-----tggtttcttactcc----tcccattact-tttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
||| | | | || | ||| |||||| || ||| || | | | ||| | || || || ||||||||||||||||||||||||| ||||| || ||||||||| |||| || || ||||||||||| || |||||||| |||| |||||||||||||||||| |||||||||
------gtatacttagttttctccacccttttt----gtgtattttggccaacatcatttagagtctgtactcttttaacctcggttcttgtttctctttcatatggcagTGTTGCTCATTTTTTGGAATCTAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACGGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: EFJ36319 (Selaginella moellendorffii), 3'ss of exon 12
agtgccaaataacaaaatcataaaaaatttcctagcagtgcattttgtcctgttgtgttttgatggtttcttactcctcccattacttttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
|| || | |||| | | || | || || |||| | | ||||||||| ||||||||||||||| | |||||||||||||| || ||||| || |||||| | ||||| | |||||||| ||||||||||| || |||
---------------------------------------------------gtaaacttgggctggtgtataacac-tctcaatactcctatt----cagTGTTGCCCATTTCTTGGAGTCACGTGGTATGCTGGAGGACGCCCTTGAAGCGGCAACTGATCCGGATTATCGATTTGACCTTGCTGTGCAACTGGGCAAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: EFJ09529 (Selaginella moellendorffii), 3'ss of exon 12
agtgccaaataacaaaatcataaaaaatttcctagcagtgcattttgtcctgttgtgttttgatggtttcttactcctcccattacttttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
|| | |||| | || | |||| | || | |||| | | || |||| ||||||| ||||||||||||||| | |||||||||||||| || ||||| || |||||| | ||||| | |||||||| ||||||||||| || |||
-------------------------------------gtaaactttggctggtact--tttgctagtataacactctcaatactcctattca-------gTGTTGCCCATTTCTTGGAGTCACGTGGTATGCTGGAGGACGCCCTTGAAGCGGCAACTGATCCGGATTATCGATTTGACCTTGCTGTGCAACTGGGCAAAMapped 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|2443004|gb|C74775.1|C74775EST: GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAA TGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
genomic: GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgct ... catatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcctgttgtgttttgatggtttcttactcctcccattacttttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
ttcttac putative branch site (score: 2)
tttcttactcctccca CT-rich tract
attacttttcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgccaaataacaaaatcataaaaaatttcctagcagtgcattttgtcctgttgtgttttgatggtttcttactcctcccattacttttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - -taacaaa
- - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - -gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - -ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgatgg