Sequence
atgc intronic sequence ATGC exonic sequence...tgctgttgaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaataccttgcttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g45670.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G118693_T02 (Zea mays), 3'ss of exon 1
tgctgttgaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaa--taccttgctt-cttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
| | |||||| || | |||| | ||| ||| | | || | || ||| | | || ||| | |||||||||||||| || || || |||||||||||||| ||||| ||||| |||||||| ||||||||||| || ||||| || || |||
-gttcttgaatccataca-ctgtcccaaaaaattgtcactgaaatataagacca-catcttgcatgtaatattcatgtgtaaactattttcttttcttttcagCTTTGACCGTGACTGGAAGAAGATAGAGGCTTTTGTTGGCTCCAAGACCGTCATCCAG
upper sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G833032_T03 (Zea mays), 3'ss of exon 1
tgctgttgaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaa----taccttgcttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
|| | |||||| || | ||| | ||| ||| | || | || ||| | | || ||| | |||||||||||||| | | ||||||| |||||||||||||| ||||| |||||||| ||||||||||| || |||||||| || |||
tgttcttgaatccatacacatgtcccaaaaatttagtg---aaatataagaccata-tcttgcatgtaatattcatgtgtaaactatgtttcttttctttttagCTTTGATCGTGACTGGAAGAAGATAGAGGCTTTTGTTGGCTCCAAGACTGTCATCCAG
upper sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G29740.1 (Glycine max), 3'ss of exon 1
tgctgttgaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaataccttgcttct--tttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
| | |||| ||| ||| | | || | || | | ||| || | | | | | | |||| |||||| ||||||||||||||||||||||| ||||| ||||||||||| |||| |||||| |||
--gtttcaaattaaagctagtgtttgtttctcccctttctttatcttggggtcgccatttgccactatcctcactttttttccccttcatttctgttttcagGTTTGATCGTGATTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAG
upper sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
-----tgctgttgaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaataccttgcttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
||| || || | || | | | ||| | | | | | | || | | || || | || | | | | | | | | |||| ||||| ||||| ||||||||||| ||||| ||||||||||| ||||| || || |||
atttaagctatttg-tttgtttttcccttttatggccttggtgccatccttttgcattatc---tcatat-tgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
upper sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G24400.1 (Glycine max), 3'ss of exon 1
tgctgttgaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacat----ctgatattcatgtgtaataccttgcttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
| |||| ||| ||| | | | | || ||| || || | ||| | ||| | | | ||||||| ||||| ||||| ||||||||||| ||||| ||||||||||| |||| |||||| |||
----ttcaaattaaagctagtgtttgtttctcccctttcttgaccttggggtctctatttgccactatcctcacattgttttgttccttcatttcttttttcagGTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAG
upper sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
--tgctgttgaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaataccttgcttcttt--tcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
||| |||| | || || | | | ||| | ||||||| ||| || | ||| | || || |||||| ||| ||||| ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| |||
tacagtgtcaaattaagataatcgtttgttttccct--tttctggccttagtatcatccttttgcatt--atctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
upper sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
---tgctgtt-gaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaataccttgcttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
|||| |||||| | || | | | || ||| | || || | | | | || ||| |||| |||| ||||| ||||||||||||||||| || || ||||||||||| ||||| |||||||||
aatcatcaccagaatgggtgtatcttttcagtttatctcttctt--attcctaattaatggattagtttccataaattgattttgtta--ttgattctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAGMapped 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|58606031|gb|CK034064.1|CK034064EST: GAGAGCTGGACGGAGCAGGAGCACGACAAGTTCCTTGAGGCCCTCCAGCT CTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGT
genomic: GAGAGCTGGACGGAGCAGGAGCACGACAAGTTCCTTGAGGCCCTCCAGCTgtaagcaaaa ... ttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGT
EST:
gi|58654476|gb|CK043156.1|CK043156EST: GAGAGCTGGACGGAGCAGGAGCACGACAAGTTCCTTGAGGCCCTCCAGCT CTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGT
genomic: GAGAGCTGGACGGAGCAGGAGCACGACAAGTTCCTTGAGGCCCTCCAGCTgtaagcaaaa ... ttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGT
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:
70 (upstream exon),
70 (downstream exon)
Score:
38AGGACGCCAGCAAGAAGGTGCGGAAGCCGTACACCATCACCAAGTCGCGCGAGAGCTGGACGGAGCAGGAGCACGACAAGTTCCTTGAGGCCCTCCAGCTgtaagcaaaa ... ttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaggactgtccttttacatctgatattcatgtgtaataccttgcttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
atctgat putative branch site (score: 38)
taccttgcttcttttc putative PPT
ttttacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctgttgaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaataccttgcttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
tgctgtt
- - - - - - - - - - -gtacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcatg