Sequence
atgc intronic sequence ATGC exonic sequence...atggactgaaccttctactcattcattacattccaaatacatttctggaaccagcactggaggctgctaatggttcttcacccaatcttctgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGGTGTTCTTGTAAAAACACCAGAAGAAGCTGTAGCTCATTTCTTTGATGTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g43390.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g43390.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G024738_T03 (Zea mays), 3'ss of exon 4
atggactgaaccttctactcattcattacattccaaatacatttctggaaccag-cactggaggctgctaatggttcttcacccaatctt--ctgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGGTGTTCTTGTAAAAACACCAGAAGAAGCTGTAGCTCATTTCTTTGATGTC
| || | || || |||||||||||||| | | ||| || | || || |||||||| ||||| | | | ||||||||||||||||| ||| ||||||||||||||||||||||||| || |||||
---aaatgggctttgcctccagtcattacattccaatttctttttggggattaggtgctatgaactgctaattattctttgtctcttactgcctgctctgcagGGTTGTGAAAGCAGCTGGTCCAAAAGGTCATATACTTAATCTGGGC------------------------------------------------------
upper sequence: LOC_Os01g43390.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G377609_T03 (Zea mays), 3'ss of exon 4
atggactgaaccttctactcattcattacattccaaatacatttctggaaccagcactggaggctgctaatggttcttca----cccaatcttctgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGGTGTTCTTGTAAAAACACCAGAAGAAGCTGTAGCTCATTTCTTTGATGTC
||| | | || | | || ||| | || | || |||| ||||||||| || || | | ||||||||||||||||| ||| |||||||| |||||||||||||||| ||||||||||| ||||| ||| |||||||| |||||||||||||| |||||||||||||||
atgctacagtacccgagggcgctcttatctcgcctaatcaagttt---agtca-cactatgaactgctaatgatttttttggtctcttactgcctgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGGTGTACTTCAGAAAACACCCGAAGAAGCTGTAGCACATTTCTTTGATGTC
upper sequence: LOC_Os01g43390.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G025031_T02 (Zea mays), 3'ss of exon 1
atggactgaaccttctactcattcattacattccaaatacatttctggaaccag-cactggaggctgctaatggttcttcacccaatctt--ctgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGGTGTTCTTGTAAAAACACCAGAAGAAGCTGTAGCTCATTTCTTTGATGTC
| || | || || |||||||||||||| | | ||| || | || || |||||||| ||||| | | | ||||||||||||||||| ||| ||||||||||||||||||||||||| || ||||||||||||| ||| |||||||| |||||||||||||| |||||||||||||||
---aaatgggctttgcctccagtcattacattccaatttctttttggggattaggtgctatgaactgctaattattctttgtctcttactgcctgctctgcagGGTTGTGAAAGCAGCTGGTCCAAAAGGTCATATACTTAATCTGGGCCATGGTGTACTTCAGAAAACACCCGAAGAAGCTGTAGCACATTTCTTTGATGTC
upper sequence: LOC_Os01g43390.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G088533_T01 (Zea mays), 3'ss of exon 4
atggactgaaccttctactcattcattacattccaaatacatttctggaaccagc-actggaggctgctaatggttcttca----cccaatcttctgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGGTGTTCTTGTAAAAACACCAGAAGAAGCTGTAGCTCATTTCTTTGATGTC
|| | || || |||||||||||||| | | ||| | | | || || ||||||||| || || | | ||||||||||||||||| ||| |||||||| |||||||||||||||| ||||||||||| ||||| ||| |||||||| |||||||||||||| |||||||||||||||
-----atgggctttacctccagtcattacattccaatttcctttttaggattagttgctatgaactgctaatgatttttttggtctcttactgcctgctctgcagGGTTGTGAAAGCAGCTGGTACAAAAGGTCATATACTTAACTTGGGCCACGGTGTACTTCAGAAAACACCCGAAGAAGCTGTAGCACATTTCTTTGATGTC
upper sequence: LOC_Os01g43390.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G024738_T03 (Zea mays), 3'ss of exon 5
atggactgaaccttctactcattcattacattccaaatacatttctggaaccagcactggaggctgctaatggttcttcacccaatcttctgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGGTGTTCTTGTAAAAACACCAGAAGAAGCTGTAGCTCATTTCTTTGATGTC
|||||||| ||| |||||||| |||||||||||||| |||||||||||
--------------------------------------------------------------------------------------------------------------------------------------------------catggTGTACTTCAGAAAACACCCGAAGAAGCTGTAGCACATTTCTTTGA----Mapped 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|86838508|gb|CI329036.1|CI329036EST: CCAGCATTTCTATTTTCTCCATTACCAGTACTGACCGATGAAATTCATAG GGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGG
genomic: CCAGCATTTCTATTTTCTCCATTACCAGTACTGACCGATGAAATTCATAGgttagttaaa ... tgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaaccagcactggaggctgctaatggttcttcacccaatcttctgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGGTGTTCTTGTAAAAACACCAGAAGAAGCTGTAGCTCATTTCTTTGATGTC
tgctaat putative branch site (score: 2)
tcttctgctct putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggactgaaccttctactcattcattacattccaaatacatttctggaaccagcactggaggctgctaatggttcttcacccaatcttctgctctgcagGGTTGTCAAATCAGCTGGTCCAAAAGGTCATATACTAAACTTGGGCCATGGTGTTCTTGTAAAAACACCAGAAGAAGCTGTAGCTCATTTCTTTGATGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA