Sequence
atgc intronic sequence ATGC exonic sequence...ttccgtatatcataacaatacacaatgatgttttaaagaaaaataaaacatgaattgtttgcatattttcaagcctgagaaccatatttctctatctcagATTCCCTGGTGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAGATGTTTATAG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os08g06880.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g06880.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G455171_T01 (Zea mays), 3'ss of exon 13
ttccgtatatcataacaatacacaatgat-gttttaaagaaaaataaaacatgaattgtttgcatattttcaagcctgagaaccatatttctctatctcagATTCCCTGGTGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGA--AGATGTTTATAG
| || | | | | | | | | | |||| || || | ||| || | || || | || | | | ||||||| | ||||||||||||||| |||||||| |||||||||| | |||| || | |||| ||| ||||| ||||| |||||||||| |
-cctctaggcgacatccagatcctgttcccgggtcaaagggaactatcatatgttttataactattccttgatctttgtgtatgttttttctctttggcagATTCCCTGGTGGGGTTACACATTCCTTCACTGACTCAACAGAAGATCAGGATAGGCTACTTTCTTTTGAGAAGATGTTTATCG
upper sequence: LOC_Os08g06880.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 7
------------------------------------------------------------------ttccgtatatcataacaatacacaatgatgttttaaagaaaaataaaacatgaattgtttgc-atattttcaagcc------tgag------aaccatatttctctatctcagATTCCCTGGTGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGA--AGATGTTTATAG
|| | | || || ||| || | | | || | || | | ||| || |||| | | ||| | | ||||||| | ||||||||||||||| |||||||| |||||||||| | ||||| || || || | ||| ||||| ||||| ||||||||||||
gtagcatataatctgtattcggtaggtggtgttcctcaatgatgccctgctggatacactcttgtttttaatgaaacagttgaaagtacactggt-tgtaggagttacctatgtttcaattcacttgttatgttttataactatttcttgatctctctgtctgtttttctctttggcagATTCCCTGGTGGGGTTACACATTCCTTCACTGACTCAGCAGAAGATCGGGACATGCTACTTTCTTTTGAGAAGATGTTTATAG
upper sequence: LOC_Os08g06880.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G081668_T02 (Zea mays), 3'ss of exon 9
-------------------------------------------------------------------------------ttccgtatatcataacaatacacaatgatgttttaaagaaaaataaaacatgaattgtttgcatattttcaagcctgagaaccatatttctctatctcagATTCCCTGGTGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGA--AGATGTTTATAG
|| || | | || | | | | | ||| || | || || | || | | ||||||| | ||||||||||||||| |||||||| |||||||||| | |||| || | |||| ||| ||||| ||||| |||||||||| |
gtagcatataatctgtattccgtaggtggtgttcctcaatgatgccctgctggatacactcttgtttttaatgaaacagttgaaagtacactggccgtaggatttacctatgtttcaattcacttgttatgttttataactattcattgatctttgtgtctgttttttctctttggcagATTCCCTGGTGGGGTTACACATTCCTTCACTGACTCAACAGAAGATCAGGATAGGCTACTTTCTTTTGAGAAGATGTTTATCG
upper sequence: LOC_Os08g06880.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G704381_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------ttccgtatatcataacaatacacaatgatgttttaaagaaaaataaaacatgaattgtttgcatattttcaagcctgagaaccatatttctctatctcagATTCCCTGGTGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGA--AGATGTTTATAG
|| || | | || | | | | | ||| || | || || | ||| | | | ||||||| | ||||||||||||||| |||||||| |||||||||| | |||| || || |||| ||| | || ||||| |||||||||| |
gtagcatataatatgtattctgtaggtggtgttcctcaatgatgccctgctggatacactcttgtttttaatgaaatagttgaaagtacactggccgtaagagttacctatgtttcaattcacttgttatgttttataactattccttgatctctgtgt-ctgtttttctctttggcagATTCCCTGGTGGGGTTACACATTCCTTCACTGACTCAACAGAAGATCGGGATAGGCTACCTTGTTTTGAGAAGATGTTTATCG
upper sequence: LOC_Os08g06880.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G455171_T01 (Zea mays), 3'ss of exon 17
------------------------------------------------------------------ttccgtatatca--taacaatacacaat-------gatgttttaaagaaaaataaaacatga-attgtttgcatattttcaagcctgagaacc-atatttctctatctcagATTCCCTGGTGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGA--AGATGTTTATAG
|| | | || | | | ||||| | | | | || | | | | || | | |||| || | | | ||||||| | ||||||||||||||| |||||||| |||||||||| | ||||| || || |||| ||| ||||| ||||| |||||||||| |
gtagcatataatctgtattccgtaggtggtgttcctcaatgatgccctgctggatacactcttgtttttaatgaaacagttgaaagtacactgtcgtaggagttacctctgtttcaattcacctgttatgttttataactattccttgatctctgtgtctgtttttctctttggcagATTCCCTGGTGGGGTTACACATTCCTTCACTGACTCCGCAGAAGATCGGGATAGGCTACTTTCTTTTGAGAAGATGTTTATCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacatgaattgtttgcatattttcaagcctgagaaccatatttctctatctcagATTCCCTGGTGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAGATGTTTATAG
tatttctctatctc CT-rich tract
atattttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttccgtatatcataacaatacacaatgatgttttaaagaaaaataaaacatgaattgtttgcatattttcaagcctgagaaccatatttctctatctcagATTCCCTGGTGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAGATGTTTATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - -aacaata
- - - - - - - - - - - - atgatgt
- - - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccata
