Sequence
atgc intronic sequence ATGC exonic sequencegtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g54340.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
| | | | | | ||| | ||| | || || ||| | ||||||| ||||||||| || || |||| | |||| | |||| | | || || |||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||||| || ||||||||||||||||| ||||| |||||||| |
------------gtatgtgatccttttttcttcttgtg--agctggcacatac---tgcatca---tagttagttacgggactagtttggt---tactctgtgct---tgtaccttttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAAGGCGTCCTTTGCTATGGCCCACCTGGCACTGGCAAGA
upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcat-caggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
||| || ||||| || || | || || | || ||| | || || | || | | | | ||||||| ||| | | | ||||| ||||||||||||||||||||| ||||||||||| || || ||||| || ||||||||||||||||| || ||||||||||| || || || ||||||||||
-----gtaagtgattggaagttcccttcattttt------aatctgtt-ataattgaggatgcaagttacatggcgcta-atttatttttttatattttatctgcta-----------------gGTTGTTGAGCTTCCCATGCTCCACCCAGAGAAATTCGTTAAGCTAGGAATTGATCCTCCAAAGGGTGTTCTTTGCTATGGTCCACCAGGGACTGGCAAAA
upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcat-caggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
|| | | | | | || | | || || | || ||| | || | | || | || | |||||| ||| | | | ||||| ||||||||||||||||||||| ||||| ||||| || || ||||| || ||||||||||||||||| || ||||||||||| || || || ||||||||||
-----------gttagtgattggaagttcccttgatttttaatctgtt-ataattgcggatgtaagttacatggtgctaattttatttatttatattttatctgcta-----------------gGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATTGATCCTCCAAAGGGTGTTCTTTGCTATGGTCCACCAGGGACTGGCAAAA
upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
| || | | || | | | || | || | | | | | | | | | ||| | | |||||||||| |||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| || ||||| |||||||| || |||||||| ||||
-------------------------------------gtaag-tcattggaatttttacttattttacatttataatgaagtagataagtcacgtgtcactaatttgtaatt--tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA
upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatt-tactgtttgctaattattgtttgttcata-gGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
| || ||| | || | || | | || || || | | | | || | ||| | ||||||||| |||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| || ||||| ||||| || || |||||||| ||||
---------------------------------------------gtaagtcattgaaatttcacttatcttacattataatgataatgaagttatgcggcactaaatttgtcatttccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA
upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 6
---------gtatactaatcttttttcagttcatatcccttgt-cgtgcaaacttgctcatccttgtgcatcaggctagtt---agttttggacttattttgctatttactgtttgctaattattgt----ttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
| | | | |||||| ||| ||| | | | | | || || | |||| | ||| |||||| | || | | | | | |||||||| || || | ||| ||||| |||||||| || ||||| ||||| ||||||||||| |||||||| ||||||||||| ||||| || || |||||||| ||||||||||| || ||||
gtgtgtatattctttttacatttttttttgtcagatcatatatgcatttacaccgtgtctttcttgattaacag-ctagtttttgatcctgtgaacttctgtccttctcttgtttgctgatatttataactttggctctagGTGGTTGAGCTCCCTATGCTCCACCCTGAGAAGTTTGTGAAGCTTGGAATTGATCCTCCTAAGGGTGTTCTCTGCTATGGTCCTCCTGGAACCGGTAAAA
upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtg-catcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
| | || | || || |||| || || || ||| ||||| | | | || || | | || | || | | |||||| || ||| | || ||| | || || |||||||| || || | || |||||||| || || || |||||||||||||||||||| ||||||||||| |
-------------------gctgatgtggtaaagatagctgtttttaaaggtagtgtggcaacaagcccgttggttttaaaggtgt--tgatacatggtaattcgtggttgtactg----aatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATTGATCCGCCCAAAGGAGTCCTTTGCTATGGCCCTCCCGGAACTGGCAAGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29684844|gb|CB681119.1|CB681119EST: CATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAG GTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
genomic: CATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAGgtatactaat ... ttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
EST:
gi|58685776|gb|CK074463.1|CK074463EST: CATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAG GTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
genomic: CATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAGgtatactaat ... ttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
EST:
gi|58600395|gb|CK010923.1|CK010923EST: GATTGAAAAAATGCGGGAG GTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
genomic: GATTGAAAAAATGCGGGAGgtatactaat ... ttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
62 (upstream exon),
70 (downstream exon)
Score:
78AATTGACCCAAGTGTTACCATGATGACAGTTGAGGAAAAACCTGATGTGACATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAGgtatactaat ... ttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
tgctaat putative branch site (score: 78)
tttgttc putative PPT
ttattttgctattta TA-rich tract