Sequence
atgc intronic sequence ATGC exonic sequence...cctgcaatatgcacttattgttttttcgtaagggaactgtttagtgtattttttatgtgtataacaccttcagttttcccatatgcaacttctttttcagTTAATTACGACAATGCGGACACTCTACCAAAAATGCAAACTGGTCCATGGTGATCTGAGTGAATACAACATTCTTTATTTCGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g06820.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G120329_T02 (Zea mays), 3'ss of exon 7
--cctgcaatatgcacttattgttttttcgtaagggaactgtttagtgtattttttatgtgtataacaccttcagttttcccata-----tgcaacttctttttcagTTAATTACGACAATGCGGACACTCTACCAAAAATGCAAACTGGTCCATGGTGATCTGAGTGAATACAACATTCTTTATTTCGAG
||| ||| | ||| || | | | | | || |||| | ||| | || |||||||||| |||| | | | ||||| ||| ||||||| ||||||||||| || ||||||| ||||||||||||||||||||| ||||||||||||| ||||| ||||| |||
gcatagcattatctatttacaattgatattt-----attttactgttggatttcat-tgtatgtattgttttcagttttctcatactacttacggcacctttt-cagATAATTACAACAATGCGGACTCTTTACCAAACGTGCAAACTGGTCCATGGTGATTTGAGTGAATACAATATTCTATATTTTGAG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 7
--cctgcaatatgcacttattgttttttcgtaagggaactgtttagtgtattttttatgtgtataacaccttcagttttcccata-----tgcaacttctttttcagTTAATTACGACAATGCGGACACTCTACCAAAAATGCAAACTGGTCCATGGTGATCTGAGTGAATACAACATTCTTTATTTCGAG----------------
||| ||| | ||| || | | | | | || |||| | ||| | || |||||||||| |||| | | | ||||| ||| ||||||| ||||||||||| || ||||||| ||||||||||||||||||||| ||||||||||||| ||||| ||||| |||
gcatagcattatctatttacaattgatattt-----attttactgttggatttcat-tgtatgtattgttttcagttttctcatactacttacggcacctttt-cagATAATTACAACAATGCGGACTCTTTACCAAACGTGCAAACTGGTCCATGGTGATTTGAGTGAATACAATATTCTATATTTTGAGGTAGTGAACCTCATAT
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G46440.1 (Glycine max), 3'ss of exon 7
cctgcaatatgcacttattgtttt---ttcgtaagggaactgtttagtgtattttttatgtgtataacaccttcagttttc-ccatatgcaacttctttttcagTTAATTACGACAATGCGGACACTCTACCAAAAATGCAAACTGGTCCATGGTGATCTGAGTGAATACAACATTCTTTATTTCGAG-
| || | ||||| |||||| || |||||| || || || |||| ||| | || | | ||||| | | ||| || | |||||| | |||| ||||||||||| | || || ||||||||| |||| || |||||||| |||||||| || || |||||||| |||
cttgatggaaacactt-ctgttttaggtttctaagggt----ttgagggtcttttccatgcatcaaataattacagttgaaatcgtgagcattttttgtttcagaTTATTATTGCAATGCGGACATTGTATCAGAAATGCAAATTGGTGCACGGTGATCTCAGTGAATATAATATACTTTATTTTGAGG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G39750.1 (Glycine max), 3'ss of exon 7
cctgcaatatgcacttattgttttttcgtaagggaactgtttagtgtattttttatgtgtataacaccttcagttttc-ccatatgcaacttctttttcagTTAATTACGACAATGCGGACACTCTACCAAAAATGCAAACTGGTCCATGGTGATCTGAGTGAATACAACATTCTTTATTTCGAG
|| || | |||| || | || | || | || ||| | || | | |||| ||| ||| || | |||||| | |||| ||||||||||| | || || ||||||||| |||| ||||||||||| |||||||| || || |||||||| |||
-tcttgatggaaacccttctcttttaggtttctaagggtttgaaggtctattccatgcatcgaataattaaagttgaaatcatgagcattttttgtttcagATTATTATTGCAATGCGGACATTGTATCAGAAATGCAAATTGGTGCATGGTGATCTCAGTGAATATAATATACTTTATTTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattttttatgtgtataacaccttcagttttcccatatgcaacttctttttcagTTAATTACGACAATGCGGACACTCTACCAAAAATGCAAACTGGTCCATGGTGATCTGAGTGAATACAACATTCTTTATTTCGAG
gtataac putative branch site (score: 3)
cttctttttc putative PPT
ttttatgtgtataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgcaatatgcacttattgttttttcgtaagggaactgtttagtgtattttttatgtgtataacaccttcagttttcccatatgcaacttctttttcagTTAATTACGACAATGCGGACACTCTACCAAAAATGCAAACTGGTCCATGGTGATCTGAGTGAATACAACATTCTTTATTTCGAG
cctgcaa
- - - atatgca
- - - -tatgcac