Sequence
atgc intronic sequence ATGC exonic sequence...ccgcgaatttcttattagttgtgtggtgtgtaccttttaaatcggaatcgggatgtaacttaatgcttaattcatattctctctcttttttttcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g54750.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G826714_T02 (Zea mays), 3'ss of exon 1
----ccgcgaatttcttattagttgtgtggtgtgtaccttttaaatcggaatcgggatgtaacttaatgcttaattcatattctctctcttttttttcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
|| ||| | || |||| || | | || | ||| | || | | || || | || | | | |||||| |||||||||||||||||||||||||| |||||||| ||||||||||| | ||||| |||||||||||||| || ||
tggaacgtaaatagactccatgtattgtg-tgaattcattattcatccttctataattgggatctgtgttttgatgtgaaccctgtga---tcgctctctgcagAGGCTTATGATTCGCTGGATCCAAATGGCAACATCACCATAAAATGGGATATCATGCAGTGGACTCCTGATGGATATGTC
upper sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 1
ccgcgaatttcttattagttgtgtggtgtgtaccttttaaatcggaatcgggatgtaactta-atgcttaattcatattctctctcttttttttct-tgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
|| | | | | | | | ||| | ||| | || | ||| | || || || || | | || | || ||| |||||| || || ||||||||||||||||| || |||||||| ||||||||||| | ||||| ||||||||||| || || ||
-aacgtaacatagacttcatatattgcgtgaattcattat-ccatcttctttctataattgggatctttgtttgatgtcaaccctgtgattgctctctgcagAGGCCTACGATTCGCTGGATCCAAACGGCAACATCACTATAAAATGGGATATCATGCAGTGGACTCCTGACGGATATGTC
upper sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G50750.1 (Glycine max), 3'ss of exon 1
ccgcgaatttcttat-tagttgtgtggtgtgtaccttttaaatcggaatcgggatgtaacttaatgcttaattcatattctctctcttttttttcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
||| | ||| |||| | | | || || || | | | ||||| | | | | || |||| |||| ||||||||| |||| || ||||||||||| || ||||| |||||||| ||||| ||||| |||||||| || ||
gtagtaatgtagtatatagtacaggaatatttagaggttcaacatttactttgtttccttttaattactttccaccagctaattgtctgttaatctttcaGATGCTTATGATCCGCTTGACCCAAATGGGAATATAACAATCAAATGGGATGTTATATCCTGGACCCCTGATGGATATGT-
upper sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 1
ccgcgaatttcttattagttgtgtggtgtgtaccttttaaatcggaatcgggatgtaacttaatgcttaattcatattctctctcttttttttcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
|| | || | || || || || ||||| |||||| | | | ||| ||| | ||| |||||||||||||| | || ||||||||||| || |||||||| |||||||| |||| ||||| |||||||| || |||
---------------------------gtatccccctc---tccccttc---atata--ttaat-tttaattttaagtttttctgtttat---ctttcagaagCTTATGATCCACTTGATCCAAATGGAAATATCACAATCAAATGGGATATTATAAGCTGGACACCTGATGGCTATGTT
upper sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 1
ccgcgaatttcttattagttgtgtggtgtgtaccttttaaatcggaatcgggatgtaacttaatgcttaattcatattctctctcttt---tttttcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
| || | || | | ||| | | || | | | | | | || | |||| || | | || | | ||| |||| |||| ||||||||| |||| || ||||||||||| |||||||| |||||||| |||| ||||| |||||||| || ||
tgtagtatataatacgaat-atgtagag-gttcgacatttacttgtcttctttcctttctgtttacttactttccacttgctaattgtctgtttatctttcaGATGCTTATGATCCGCTTGACCCAAATGGGAATATCACAATCAAATGGGATATTATAAGCTGGACCCCTGATGGATATGT-
upper sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 1
ccgcgaatttcttattagttgtgtggtgtgtacctt-ttaaatcggaatcgggat-gtaacttaatgcttaattcatattctctctcttttttt-tcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
| | | ||| || || ||| || ||| | || | || ||||| | | || || || | | | | ||| |||| |||||||||||||| | || |||||| |||| || |||||||| |||||||| | || ||||| ||||||||||| |||
-tataagaagcct--taggggttcattgattactttgccaaacccctctccccttcatatattaattttaatttaattttgagtttttctgtttatctttcagAAGCTTATGATCCACTTGATCCATATGGAAATATCACAATCAAATGGGATATCATAAGTTGGACCCCTGATGGTTATGTT
upper sequence: LOC_Os03g54750.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 1
----ccgcgaatttcttattagttgtgtggtgtgtaccttttaaatcggaatcgggatgtaacttaatgcttaattcatattctctctcttttttttcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
| || | ||| ||||| | | | || | | | | | |||| || | | || || || | | | | |||||||||| |||||| |||| |||||| | || ||||| ||||| |||||||| |||||| |||||||||||||| || |||
ctacaaaccaaataattagtagttttaagat-tgaagcaatca---caatgtcggtgtggatcaggataaacaaagttctgacttttggtaaatccttttgcagAAGCATATGATGCGCTTGATCCAGAAGGCAACATTACAATGAAATGGGATGTTATGAGCTGGACTCCTGATGGCTATGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcgggatgtaacttaatgcttaattcatattctctctcttttttttcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
cttaattcatattctc CT-rich tract
ttaattcatattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccgcgaatttcttattagttgtgtggtgtgtaccttttaaatcggaatcgggatgtaacttaatgcttaattcatattctctctcttttttttcttgcagAAGCTTATGATTCGCTGGATCCAAATGGGAACATCACAATAAAATGGGACGTTATGCAATGGACTCCTGATGGTTACGTT
- - - - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttaa