Sequence
atgc intronic sequence ATGC exonic sequencegtttggttccttgtcttctcttcataaacagtaaacagtagaacatttcttgagcaaatatgtcgcttaattcgcggcatctttttttttccagACGTGAAAGGCTAGTGGTACATGAATCATCAAATATTGTCATAACAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g25370.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g25370.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G088653_T03 (Zea mays), 3'ss of exon 2
gtttggttccttgtcttctcttcataaacagtaaacagtagaacatttcttgagcaaatatgtcgcttaattcgcggcatctttttttttccagACGTGAAAGGCTAGTGGTACATGAATCATCAAATATTGTCATAACAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAG
| || ||| |||||| || | || | | | | | | | | | | ||| || || | | |||||||||| ||| ||| ||| ||||||||| | ||||||||||| ||||| || |||| | ||||||||||||| | |||||||||||||||||||
----gtttgcttatcttcttttgtcatttgatagtcgcacggatgtctacttaactagt-tgtatctaaaaggg---------tccttttccagACATGAGAGGTTAGCAGTACATGAACCTTCAAATATTGTGATAACGAGGGAGATCATGCAGTGCTTGAATAACCAGGAGTGGCTAAATGATGAG
upper sequence: LOC_Os01g25370.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G012601_T02 (Zea mays), 3'ss of exon 2
gtttggttccttgtcttctcttcataaacagtaaacagtagaacatttcttgagcaaatatgtcgcttaattcgcggcatctttttttttccagACGTGAAAGGCTAGTGGTACATGAATCATCAAATATTGTCATAACAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAG
||||| || || |||||| || || || || || | | | | | || || || | | ||| | ||| ||||| ||| ||| ||||||||| | ||||||||||| |||||||| |||| |||||| |||||||| | ||| |||||||||||||||
gtttgcttt-ttatcttcttttgttatgtgatagtcacacaaatgcctacataactagtg-gtatctaaaagtg--------tcctttatgcagTCGTGAGAGGTTAGCAGTACATGAACCTTCAAATATTGTGATAACAAGGGAGATCTTGCAATGCTTGAATAACCAGGAATGGCTAAATGATGAGMapped 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|428598|gb|D24750.1|D24750EST: ACGGATGAGGATGAGGATAGTGTTGATCATGCTCTTGGTGGCCGTAACAG ACGTGAAAGGCTAGTGGTACATGAATCATCAAATATTGTCATAACAAGAGA
genomic: ACGGATGAGGATGAGGATAGTGTTGATCATGCTCTTGGTGGCCGTAACAGgtttggttcc ... ttttttccagACGTGAAAGGCTAGTGGTACATGAATCATCAAATATTGTCATAACAAGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaacatttcttgagcaaatatgtcgcttaattcgcggcatctttttttttccagACGTGAAAGGCTAGTGGTACATGAATCATCAAATATTGTCATAACAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAG
gcttaat putative branch site (score: 4)
catctttttttttcc putative PPT
atcttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggttccttgtcttctcttcataaacagtaaacagtagaacatttcttgagcaaatatgtcgcttaattcgcggcatctttttttttccagACGTGAAAGGCTAGTGGTACATGAATCATCAAATATTGTCATAACAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA