Sequence
atgc intronic sequence ATGC exonic sequence...gaagttgctggcctattgtgcttcttcttcttctttttttcctgaaatcgggctccttgttgcgttctcaatttgatggtgggtactctcttttgtgtagGATTCTGGCGAACAGGCAATCGGCGGCGAGGTCGAAGGAGAGGAAGATCAAGTACACCGGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g06170.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g06170.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G079365_T01 (Zea mays), 3'ss of exon 1
------------------------gaagttgctggcctattg----tgcttcttcttcttctt----tttttcctgaaatcgggct------ccttgttgcgt---------tctcaatttgatggtgggtac--tctctttt---------gtgtagGATTCTGGCGAACAGGCAATCGGCGGCGAGGTCGAAGGAGAGGAAGATCAAGTACACCGGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCA
|| || | ||| |||||| | || ||| | ||| || | ||| |||||| | || ||| | | | |||| | || | | ||| ||||| ||||||||| |||| || ||||||||||| |||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||
gtgagcaaacgccttcagcgtccgcgagctgtcttcaccttggaattgcttcccccgctgcttgagatgcttcatggagctgggacgtgataccttgtcctgcctggtcaagtcctggtttcaagataggtataatttcctctcccgcggcggtgcagGATCCTGGCGAACCGGCAGTCCGCGGCGAGGTCCAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCC
upper sequence: LOC_Os11g06170.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G821024_T01 (Zea mays), 3'ss of exon 1
gaagttgctggcctattgtgcttcttcttcttctttttttcctgaaatcgggctccttgttgcgttctcaatttgatggtgggt----actctcttttgtgtagGATTCTGGCGAACAGGCAATCGGCGGCGAGGTCGAAGGAGAGGAAGATCAAGTACACCGGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCA
||| | | | | ||| | | | ||| | | ||| | ||| ||| ||||| |||| || || ||||| ||||||||| |||| || ||||||||||| |||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||
---gtttcaagatccgtatccttgtcgcgcgttgaatttcttctggtccaagtgaggtgtaactatct-ggtttcgcggtggtcctcgactcctcgttctgcagGATCCTGGCGAACCGGCAGTCTGCGGCGAGGTCCAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCC
upper sequence: LOC_Os11g06170.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G09140.1 (Glycine max), 3'ss of exon 1
gaagttgctggcctattgtgcttcttcttcttctttt--tttcctgaaatcgggctccttgttgcgtt----ctcaatttgatggtgggtactctcttttgtgtagGATTCTGGCGAACAGGCAATCGGCGGCGAGGTCGAAGGAGAGGAAGATCAAGTACACCGGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCA
| || || || | | | | | | |||| | || ||| | | || ||| || || | | | || |||||||| || ||||||||||| || || || || |||||||||||||| ||||| ||||| ||||||||||||||||||| || ||||| || |||
-----agttgtgttaatgggtatatggattgtgggaaaactggaagaaaatgattggtctgatgcactgatattggcttggatttgggatattgtgggct-tgcagGATTCTTGCTAACAGGCAATCTGCTGCAAGATCCAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCA
upper sequence: LOC_Os11g06170.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G43700.1 (Arabidopsis thaliana), 3'ss of exon 1
gaagttgctggcctattgtgcttcttcttcttctttttttcctgaaatcgggctccttgttgcgttctcaatttgatggtgggtactctcttttgtgtagGATTCTGGCGAACAGGCAATCGGCGGCGAGGTCGAAGGAGAGGAAGATCAAGTACACCGGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCA
|| | || ||| || || | || | | | | | | ||| | | | || | | || | || | |||| ||||||| | ||||| || ||||| |||||||||||||| ||||||||||| | ||| || |||||| | ||||||||||| ||||| || |||| || ||
---gtatataatttagtgttgttttttacttaaagcttgtaacttttttgtgatt-tgattgaggtttgaaatag-tgttttgtgatgggtttttgatagGATTTTAGCGAATAGACAATCTGCGGCGAGGTCGAAAGAGAGGAAGATTAGGTATACTGGTGAGTTAGAGAGGAAGGTTCAGACACTTCAGAATGAAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcgggctccttgttgcgttctcaatttgatggtgggtactctcttttgtgtagGATTCTGGCGAACAGGCAATCGGCGGCGAGGTCGAAGGAGAGGAAGATCAAGTACACCGGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCA
atttgat putative branch site (score: 5)
tactctctttt putative PPT
aatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagttgctggcctattgtgcttcttcttcttctttttttcctgaaatcgggctccttgttgcgttctcaatttgatggtgggtactctcttttgtgtagGATTCTGGCGAACAGGCAATCGGCGGCGAGGTCGAAGGAGAGGAAGATCAAGTACACCGGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG