Sequence
atgc intronic sequence ATGC exonic sequence...gagggagtaatattgtgatgcttatcctgcttctcaattatcagtaatgctaagatcacactgttcttatcgtccagttcttgtctatcactttgttcagGTGGACAACACTGATGCAGAAGGAAGGCTTACACTTGCTGATGCTTTGGTATATGCCTGTAAACTGGGTGTTGACAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g24650.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g24650.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G043893_T01 (Zea mays), 3'ss of exon 6
-------------gagggagtaatattgtgatgcttatcctgcttctcaattatcagtaatgctaagatcacactgttcttatcgtccagttcttgtctatcactttgttcagGTGGACAACACTGATGCAGAAGGAAGGCTTACACTTGCTGATGCTTTGGTATATGCCTGTAAACTGGGTGTTGACAAG
| |||| || | | | | | || | | | | | | | || || ||| || | || | | | | || ||||||| || ||||| ||||| || || ||||||||||| ||||| |||||||| ||||| ||||| | ||||||||||||
gtacatattttctcttgcagtagtaacgcgtttcagaacccgtcattgtcctgctaat--ttcgtagcgttcattgtctttgtattcatatgttagcacacatgcttcttcagGTAGATAACACGGATGCGGAGGGGAGGCTTACACTGGCTGACGCTTTGGTCTATGCTTGTAACCAAGGTGTTGACAAG
upper sequence: LOC_Os12g24650.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 6
--gagggagtaatattgtgatgcttatcctgcttctcaattatcagtaatgctaagatcacactgttcttatcgtccagttcttgt----ctatcactttgttcagGTGGACAACACTGATGCAGAAGGAAGGCTTACACTTGCTGATGCTTTGGTATATGCCTGTAAACTGGGTGTTGACAAG
||||| | | | | | || | | | || ||| | || | || ||| || | | | | | | || || || |||| ||||||||||||| ||||| || ||||| || || |||||| |||||||||| ||||| | |||||||| |||
ttattggagt--tttggcctcgatgatttatttaatagaacatgtgtagtact----ttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG
upper sequence: LOC_Os12g24650.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G08150.1 (Glycine max), 3'ss of exon 6
gagggagtaatattgtgatgcttatcctgcttctcaattatcagtaatgctaagatcacactgttcttatcgtccagttcttgt----ctatcactttgttcagGTGGACAACACTGATGCAGAAGGAAGGCTTACACTTGCTGATGCTTTGGTATATGCCTGTAAACTGGGTGTTGACAAG
| | || || | || | | | | || || | || | || | |||||| | | | | | | || || || |||| ||||||||||||| ||||| || ||||| || || |||||| |||||||||| ||||| | |||||||| |||
---taattggagttttggccttgatgatttatttaatataacatgtgtagtact-ttaccccgttcttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAATCAAGGTGTTGAAAAG
upper sequence: LOC_Os12g24650.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 6
gagggagtaatattgtgatgcttatcctgcttctcaattatcagtaatgctaagatcacactgttcttatcgtccagttcttgt----ctatcactttgttcagGTGGACAACACTGATGCAGAAGGAAGGCTTACACTTGCTGATGCTTTGGTATATGCCTGTAAACTGGGTGTTGACAAG
| | || || | || | | | | || || | || | || | |||||| | | | | | | || || || |||| ||||||||||||| ||||| || ||||| || || |||||| |||||||||| ||||| | |||||||| |||
---taattggagttttggccttgatgatttatttaatataacatgtgtagtact-ttaccccgttcttgtactgaggatttgataggcttaacatcttccctagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAATCAAGGTGTTGAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgctaagatcacactgttcttatcgtccagttcttgtctatcactttgttcagGTGGACAACACTGATGCAGAAGGAAGGCTTACACTTGCTGATGCTTTGGTATATGCCTGTAAACTGGGTGTTGACAAG
ctttgttc CT-rich tract
ttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagggagtaatattgtgatgcttatcctgcttctcaattatcagtaatgctaagatcacactgttcttatcgtccagttcttgtctatcactttgttcagGTGGACAACACTGATGCAGAAGGAAGGCTTACACTTGCTGATGCTTTGGTATATGCCTGTAAACTGGGTGTTGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - -tgatgct
- - - - - - - - - - - - - -tgcttct
- - - - - - - - - - - - - - - - - - - - - - - atgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttctt