Sequence
atgc intronic sequence ATGC exonic sequencegtgaggaaaagaacttgaggtgatcaagctcgcatttccatggcagGTACTTGGCTCCAGAGTACTTCATGCACGGCAAGGTCAGCGACAAGATCGACGTGTACGCCTTCGGCGTCGTCCTCCTCGAGCTCGTCTCCGGGAGGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g07990.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g07990.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G418432_T01 (Zea mays), 3'ss of exon 6
---------------------------------------gtgaggaaaagaacttga-ggtgatcaagctcgcatttc----catggcagGTACTTGGCTCCAGAGTACTTCATGCACGGCAAGGTCAGCGACAAGATCGACGTGTACGCCTTCGGCGTCGTCCTCCTCGAGCTCGTCTCCGGGAGGAAG
| | | || || | | || | | | | || |||||||| ||| | ||||| ||||||||||||||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| |||||||||||||||||||||
gtgcgcagcgcttttcggtcatcttttcggtcctactatctaaacacaataatcagctgacgaacgtggatgtctctcttggcatggcagATACCTTGCTCCGGAGTACTTCATGCACGGCAAGGTGAGCGAGAAGATGGACGTGTACGCGTTCGGCGTCGTGCTCCTGGAGCTCGTCTCCGGGAGGAAG
upper sequence: LOC_Os12g07990.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G77280.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------gtgaggaaaagaacttgaggtgatc-------aagctcgcatttccatggcagGTACTTGGCTCCAGAGTACTTCATGCACGGCAAGGTCAGCGACAAGATCGACGTGTACGCCTTCGGCGTCGTCCTCCTCGAGCTCGTCTCCGGGAGGAAG
| | |||| | | || || || || ||| || ||| |||||||||||||||||||||||| | || ||||| | || ||||| || ||||| || |||||||| || ||||||||| | | || || || ||
gtatgaagtactctaggttttgggtaatgtttcatgaaagttcttgaaaatgttcttgtgctaatcttctgtttttgtg-cagATACTTGGCTCCAGAGTACTTCATGTATGGTAAGGTGAATGATAAGATAGATGTGTATGCATTCGGCGTTGTTCTCCTCGAGTTACTTTCGGGAAGAAAA
upper sequence: LOC_Os12g07990.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S242_29V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------gtgaggaaaagaacttgaggtg-atcaagctcgcatt---tccatggcagGTACTTGGCTCCAGAGTACTTCATGCACGGCAAGGTCAGCGACAAGATCGACGTGTACGCCTTCGGCGTCGTCCTCCTCGAGCTCGTCTCCGGGAGGAAG
|| |||| | | || || || || | |||||||||||| || || ||||||||| | || | ||| | |||||||||||| |||||||| ||||| || || || | ||||| || | || |||||
gggtgtgggattaaactgtggcgctttcctgcagccactgtatcatcgacgtagcagtcgatcgttgatacataactgactggcgttatatctctaccagGTACTTGGCCCCGGAATACTTCATGTATGGGAGGGTGAACGACAAGATCGATGTGTACGCATTCGGTGTAGTGCTTTTAGAGCTTATCACGGGTAGGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaggaaaagaacttgaggtgatcaagctcgcatttccatggcagGTACTTGGCTCCAGAGTACTTCATGCACGGCAAGGTCAGCGACAAGATCGACGTGTACGCCTTCGGCGTCGTCCTCCTCGAGCTCGTCTCCGGGAGGAAG
catttcc CT-rich tract
aaaagaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggaaaagaacttgaggtgatcaagctcgcatttccatggcagGTACTTGGCTCCAGAGTACTTCATGCACGGCAAGGTCAGCGACAAGATCGACGTGTACGCCTTCGGCGTCGTCCTCCTCGAGCTCGTCTCCGGGAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA