Sequence
atgc intronic sequence ATGC exonic sequence...cttcctccagatttaggaaacaaagagcatagtttctatgtgcacagtcatgtcttgtttaatgtgctgatttgttctgtttgtttgtcttccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATCATTGAGCGAGACATATTAAGTGAAATGGTTAAGATAGTAAAGAAAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g09329.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g09329.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G151050_T01 (Zea mays), 3'ss of exon 3
cttcctccagatttaggaaacaaagagcatagtttctatgtgcacagtcatgtcttgtttaat-gtgctgatttgttctgtttgtttgtcttccttt--tcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATCATTGAGCGAGACATATTAAGTGAAATGGTTAAGATAGTAAAGAAAAAG
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agttttggaaaattatgaa-cataaagcttagctttt--gctgatgttcatgcttctttcctttgagctgatgtgatgattccgacttgttcccttacatcagGTGCTAGAGACTCTAAGCAAAAATTGTGGGGATATTGTTCATCAACAGATTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG
upper sequence: LOC_Os11g09329.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G011315_T01 (Zea mays), 3'ss of exon 3
cttcctccagatttaggaaacaaagagcatagtttctatgtgcacagtcatgtcttgtttaat-gtgctgatttgttctgtttg--tttgtcttccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATCATTGAGCGAGACATATTAAGTGAAATGGTTAAGATAGTAAAGAAAAAG
|| | | | || ||| | | | ||| || | | | ||||| | || | | |||||| || | | || || || | ||||||||||||||||||||||||||| ||||||||| ||||| | || || || ||||||| |||||||| ||||||||| |||||||||| |||||||||
atttttagaaaattgtgaa-tatggcacgtagctttt--gctgatgttcatgcttctttcctttgagctgatgtgatgattctgacttgatcccttatgtcagGTGCTAGAGACTCTAAGCAAAAATTGTGGGGATATTGTTCATCAACAGATAGTTGAGCGTGACATATTGAGTGAAATGATTAAGATAGTGAAGAAAAAG
upper sequence: LOC_Os11g09329.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G12570.1 (Glycine max), 3'ss of exon 3
cttcctccagatttaggaaacaaagagcatagtt-tctatgtgcacagtcatgtcttgtttaatgtgctgatttgttctgtttgtttgtcttccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATCATTGAGCGAGACATATTAAGTGAAATGGTTAAGATAGTAAAGAAAAAG
| | | | || ||| ||| | | || | ||| || |||| | || | | || || || || | | |||| || ||||| || || ||||| ||||| || ||| | ||||| ||| |||||||||| || ||| |||||||||||||||||||||||| |||
ggtgcagaatacttttaaaa-aaaaatcttatccatatatttgtacagatggttacaaaaagcaatgattacctgacatgggtgctttgtatttgatctagGTACTGGAGACCCTTAGTAAAAATTGTGGTGAAAGTGTATTTCAGCAGATCGTTGAGCGAGATATCTTACATGAAATGGTTAAGATAGTAAAGAAGAAG
upper sequence: LOC_Os11g09329.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G42250.1 (Glycine max), 3'ss of exon 3
-cttcctccagatttaggaaacaaagagcatagtttctatgtgcacagtcatgtcttgtttaatgtgctgatttgttctgt-ttgtttgtcttccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATCATTGAGCGAGACATATTAAGTGAAATGGTTAAGATAGTAAAGAAAAAG
| | | | || ||| || | || | || || ||| | || | | || || || ||||| || | | |||| | |||||||| || || || ||||| || ||| | ||||| ||||||||||| || || ||| |||||||||||||||||| ||||| |||
aggtgtacaatactttaaaaaagaaaattatc-catagatttgtgcaggtggttacaaaaagcaatgattacctgacatgggttctttgtatttgatct-agGTATTGGAGACTCTTAGTAAGAATTGTGGTGAAAGTGTATTTCAGCAGATCATTGAGCGGGATATCTTACATGAAATGGTTAAGATAGTGAAGAAGAAGMapped 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|117217057|gb|CT845328.1|CT845328EST: AGAAACGCCTGGGAAACAAGAATTCAAAAGTGCAAATTCTGACGCTTTAT GTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATC
genomic: AGAAACGCCTGGGAAACAAGAATTCAAAAGTGCAAATTCTGACGCTTTATgtgagtattt ... tccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATC
EST:
gi|33654658|gb|CF277272.1|CF277272EST: AGAAACGCCTGGGAAACAAGAATTCAAAAGTGCAAATTCTGACGCTTTAT GTGCTAGAGACTCTAAGCAAAAACTGGGGGGATGGTGGTTACCAGCAAATC
genomic: AGAAACGCCTGGGAAACAAGAATTCAAAAGTGCAAATTCTGACGCTTTATgtgagtattt ... tccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATC
EST:
gi|58660357|gb|CK049037.1|CK049037EST: AGAAACGCCTGGGAAACAAGAATTCAAAAGTGCAAATTCTGACGCTTTAT GTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATC
genomic: AGAAACGCCTGGGAAACAAGAATTCAAAAGTGCAAATTCTGACGCTTTATgtgagtattt ... tccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATC
EST:
gi|88311167|gb|CI570241.1|CI570241EST: AGAAACGCCTGGGAAACAAGAATTCAAAAGTGCAAATTCTGACGCTTTAT GTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTAC-AGCAAATC
genomic: AGAAACGCCTGGGAAACAAGAATTCAAAAGTGCAAATTCTGACGCTTTATgtgagtattt ... tccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATC
EST:
gi|86901649|gb|CI310411.1|CI310411EST: AAATTCTGACGCTTTAT GTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATC
genomic: AAATTCTGACGCTTTATgtgagtattt ... tccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATC
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:
74 (upstream exon),
68 (downstream exon)
Score:
9ACAAGCCAAGGATACACTCAAGCTCCTAAAGAAACGCCTGGGAAACAAGAATTCAAAAGTGCAAATTCTGACGCTTTATgtgagtattt ... tccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATCATTGAGCGAGACATATTAAGTGAAATGGTTAAGATAGTAAAGAAAAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtcatgtcttgtttaatgtgctgatttgttctgtttgtttgtcttccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATCATTGAGCGAGACATATTAAGTGAAATGGTTAAGATAGTAAAGAAAAAG
tgctgat putative branch site (score: 9)
tttgttctgtttgttt CT-rich tract
ttgtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcctccagatttaggaaacaaagagcatagtttctatgtgcacagtcatgtcttgtttaatgtgctgatttgttctgtttgtttgtcttccttttcagGTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATCATTGAGCGAGACATATTAAGTGAAATGGTTAAGATAGTAAAGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA