Sequence
atgc intronic sequence ATGC exonic sequencegtacagcagatatctgtttccattgattatacatcggcatatctcacaacatatgtgatatatttttaactccatgattttcattatgtttataaaattttgtggccttctttcgttccagTAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTGAGTCTATTCGAGCAGTTGGGAAAATAGCGCTGCAGCAGTATGATGTGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g43630.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AC198725.4_FGT007 (Zea mays), 3'ss of exon 7
gtacagcagatatctgtttccattgattatacatcggcatatctcacaacatatgtgatatatttttaactccatgattttcattatgtttataaaattttgtggccttctttcgttccagTAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTGAGTCTATTCGAGCAGTTGGGAAAATAGCGCTGCAGCAGTATGATGTGAA
|| | | | | || || | || |||||| |||| |||| | ||| |||||| |||| ||| | || ||| ||||| || || |||||||||| ||||| |||||||||||||| || ||| | |||||||| || |||||||| |||||||| ||||||||||||||||| ||
--------------------------gtaaatgccag-acttccaactgta-atttgatatgtttt--actcattcattaccattat-tttaaaaagcatg------tttcttcccaccagTCACCGAACTGTGTGAATACGCTGGGAATGTTGATGTACCGATTGCAAGGGAGTCTATCCGCGCAGTTGGAAAAATAGCACTGCAGCAGTATGATGTTAA
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G029077_T01 (Zea mays), 3'ss of exon 5
gtacagcagatatctgtttccattgattatacatcggcatatctcacaacatatgtgatatatttttaactccatgattttcattatgtttataa----aattttgtggccttctttcgttccagTAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTGAGTCTATTCGAGCAGTTGGGAAAATAGCGCTGCAGCAGTATGATGTGAA
|| | ||| | || || || | | || |||||| |||| || | ||| ||||| |||| || |||||| ||||||| ||||| ||||| | |||||||||||||||||||||||||||||||| ||| | |||||||| || |||||||| |||||||| ||||||||||||||||| ||
---------------gtatatgcctgatattc-----tatttccaactata-atttgatatgtttt---cttattaattactattatttttaaaatatcgattttgcatgtttctttc-caccagTCACTGAACTATGTGAATATGCTGGAAATGTTGATGTACCAATTGCAAGAGAGTCTATCCGGGCAGTTGGAAAAATAGCACTGCAGCAGTATGATGTTAA
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA04G08480.1 (Glycine max), 3'ss of exon 5
--gtacagcagatatctgtttcc------attgattatacatcggcatatctcac--aacatatgtgatatatttttaactccatgattt----tcattatgtttataaaat-tttgtggccttctt-----tcgttccagTAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTGAGTCTATTCGAGCAGTTGGGAAAATAGCGCTGCAGCAGTATGATGTGAA
| | || || | | || ||| || || | | || || || | | || | ||| || | | |||| | | | || |||||| || || |||| || || || ||||||||||||| ||||||||| | || || ||| | || || |||||||| |||||||| ||||| |||||||||||||||| ||
gtaagtaacttcaatttgctatagagagaaatggttaggggaaggagtaattgatgtaagatttgcatttggtgttctattccctggtctgaggctgcccgtcttatgacttactcatgaacttcttggatctcatttcagTGACAGAATTATGTGAATATGCTGCAAATGTTGACATTCCCATTGCAAGGGAATCAATTCGAGCTGTTGGGAAGATAGCATTGCAGCAGTATGATGTCAA
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G08590.1 (Glycine max), 3'ss of exon 5
gtacagcagatatctgttt-ccattga---------ttatacatcggcatatctcac--aacatatgtgatatatttttaactccatgattt----tcattatgtttataaaat-tttgtggccttctt-----tcgttccagTAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTGAGTCTATTCGAGCAGTTGGGAAAATAGCGCTGCAGCAGTATGATGTGAA
| | | || ||| | || || ||| || | | || || || | || || | ||| || | | |||| | || || || |||||| || || |||| || || || ||||||||||||| ||||||||| | || || ||| | || || |||||||| |||||||| ||||| |||||||||||||||| ||
--gtaagaaacttcaatttgctatagagagaaagggttaggggagggagcgattgatttaagatttgcatttgatgttctattccctggtctgaggctgcctgtcttatgacatattcatgaacttcttggatctcatttcagTGACAGAATTATGTGAATATGCTGCAAATGTTGACATTCCCATTGCAAGGGAATCAATTCGAGCTGTTGGGAAGATAGCATTGCAGCAGTATGATGTCAA
upper sequence: LOC_Os01g43630.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv04s0008g03880.t01 (Vitis vinifera), 3'ss of exon 5
--gtacagcagatatct-gtttccattgattatacat-cggcatatct-cacaa-----catatgtgatatatttttaac--tccatgattttcattatg---tttataaaat------tttgtggccttctt----tcgttccagTAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTGAGTCTATTCGAGCAGTTGGGAAAATAGCGCTGCAGCAGTATGATGTGAA
|| | |||| ||| || | | || | |||| | || | | || | | |||| ||| ||||| || ||| | || | |||| ||| || | || |||| || || || ||||||||||||| |||||||||| | || || ||| | ||||| || || || |||||||||||||| ||||||||||||||||||||
gtaagcaaataacatctcattttcactaaagcctcacatgaaatatttgcatgagtaactgtgcgttctgtccttttggtgacccacctttttctccataaactttcaagtatgactgatgtgtgatcttattgagtccattacagTGACGGAATTATGTGAATATGCTGCAAATGTTGATATTCCCATTGCAAGAGAGTCAATCCGGGCTGTTGGGAAAATAGCACTGCAGCAGTATGATGTGAAMapped 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|66915427|gb|CX102275.1|CX102275EST: ACTTGAGATGCTGACTGCTATAGCAAACGAGAGCAACACCTATGAAATTG TAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTG
genomic: ACTTGAGATGCTGACTGCTATAGCAAACGAGAGCAACACCTATGAAATTGgtacagcaga ... ttcgttccagTAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taactccatgattttcattatgtttataaaattttgtggccttctttcgttccagTAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTGAGTCTATTCGAGCAGTTGGGAAAATAGCGCTGCAGCAGTATGATGTGAA
ttttaac putative branch site (score: 2)
ccttctttcgttcc putative PPT
atgattttcattatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagcagatatctgtttccattgattatacatcggcatatctcacaacatatgtgatatatttttaactccatgattttcattatgtttataaaattttgtggccttctttcgttccagTAACTGAGTTGTGTGAATATGCTGGAAATGTTGATGTACCAATCGCACGTGAGTCTATTCGAGCAGTTGGGAAAATAGCGCTGCAGCAGTATGATGTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG