Sequence
atgc intronic sequence ATGC exonic sequence...ttgatgctaccttctctcctttgatgtcaataatctaccagcttatagattttgctgcaattttttgtgagtgatcggtattgttataattaaattgcagAGGCAATGTGGCAGATGAATCTAGGAGAAGCTATGGAAGCTGGGCCATACCCAGAGCGTATTGGAGAACCAGATTGTAGTTATTACATGAGGACTGGCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os11g28270.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G146514_T02 (Zea mays), 3'ss of exon 1
ttgatgctaccttctctcctt-tgatgtcaataatctacca-gcttatagattttgctgcaattttttg-tgagtgatcg---gtattgttataattaaattgcagAGGCAATGTGGCAGATGAATCTAGGAGAAGCTATGGAAGCTGGGCCATACCCAGAGCGTATTGGAGAACCAGATTGTAGTTATTACATGAGGACTGGCTT
| || | || ||||||| | || ||| | || | ||| | | || |||||||||||| ||| || ||||||||| || | |||||||||| ||||||||||||||| | | |||||| |||||| |||||||||||||||||| |||| || ||||| ||||| |||||||||||||||||| |
----ttctgctttatctccttatcatctcagcatcatataacacttctgg--ttagctgcaatttttaaatgaacaattactaatattgttatgtttcagttgcagAGGCGATGTGGCAGATGAATTTGGAAGAAGCCATGGAACTGGGGCCATACCCAGAGCGTGTTGGTGAGCCAGACTGTAGCTATTACATGAGGACTGGCAT
upper sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G100794_T01 (Zea mays), 3'ss of exon 1
----ttgatgctaccttctctcctttgatgtcaataatctaccagcttatagattttgctgcaattttttgtgagtgatcg---gtattgttataattaaattgcagAGGCAATGTGGCAGATGAATCTAGGAGAAGCTATGGAAGCTGGGCCATACCCAGAGCGTATTGGAGAACCAGATTGTAGTTATTACATGAGGACTGGCTT
| | | || |||| | | || || || || || | ||| |||||| ||| ||||| || |||| |||| || | | |||| || ||||||||||||||| ||||||| || |||||| |||||||||||||||||| |||| || ||||| ||||| ||||||||||||||
ttctgcatttttgctttgtctcatcatctcaggatcatataacacttttctggttt-gctgcattttgaaatgagtaattactaatatttttatgtttcagTCACAGAAGCGATGTGGCAGATGAATTTAGGAGATGCCATGGAACTGGGGCCATACCCAGAGCGTGTTGGTGATCCAGACTGTAGCTATTACATGAGGAC------
upper sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G146514_T03 (Zea mays), 3'ss of exon 1
--ttgatgctaccttctctcctt-tgatgtcaataatctacca-gcttatagattttgctgcaattttttg-tgagtgatcg---gtattgttataattaaattgcagAGGCAATGTGGCAGATGAATCTAGGAGAAGCTATGGAAGCTGGGCCATACCCAGAGCGTATTGGAGAACCAGATTGTAGTTATTACATGAGGACTGGCTT
| || | || ||||||| | || ||| | || | ||| | | || |||||||||||| ||| || ||||||||| || | |||||||||| ||||||||||||||| | | |||||| |||||| |||||||||||||||||| |||| || ||||| ||||| ||||||||||||||
ctgcatttctgctttatctccttatcatctcagcatcatataacacttctgg--ttagctgcaatttttaaatgaacaattactaatattgttatgtttcagTTGCAGAGGCGATGTGGCAGATGAATTTGGAAGAAGCCATGGAACTGGGGCCATACCCAGAGCGTGTTGGTGAGCCAGACTGTAGCTATTACATGAGGAC------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagattttgctgcaattttttgtgagtgatcggtattgttataattaaattgcagAGGCAATGTGGCAGATGAATCTAGGAGAAGCTATGGAAGCTGGGCCATACCCAGAGCGTATTGGAGAACCAGATTGTAGTTATTACATGAGGACTGGCTT
tattgttataattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgatgctaccttctctcctttgatgtcaataatctaccagcttatagattttgctgcaattttttgtgagtgatcggtattgttataattaaattgcagAGGCAATGTGGCAGATGAATCTAGGAGAAGCTATGGAAGCTGGGCCATACCCAGAGCGTATTGGAGAACCAGATTGTAGTTATTACATGAGGACTGGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - tgctacc
- - - - - - - - - - ttgatgt
- - - - - - - - - - - - - - - - - -taccagc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgctgca