Sequence
atgc intronic sequence ATGC exonic sequencegtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaacaatctttattttatgtggtcttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g56000.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 8
gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaacaatctttattttatgtggtcttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
||| | || | || | || | | || | | || ||| || | || || ||| || | | |||| | || | | ||||||| || || ||||||||||| || || ||||||||||||||||||||||| || || || || || |||||||| || || || ||||| ||||| |
-------------aataagaaagggattctagcccccctccaatccccttcggttttgtggctcccaaactagcactaaaggtt------ccaaaataacgccgatctatgttgtgt-------------agATCCACTCGAGGAAAATGAATGTGAATCCAGATGTCAACTTTGAAGAGTTGGCGCGTTCAACCGATGATTTCAATGGCGCTCAGCTAAAGGCTGTTTGCG
upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 8
gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaacaatctttattttatgtggtctt---actctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
|| | |||||||| | | | |||||| | | || | |||| | | | | | || | | |||||||||| || || |||||||| |||| ||||||||||||||||| | || || || || || || |||||||| || ||||||||||| |||||||
----------------------------------------------------gtttggtgtctttaaacttcatctgctgacttgtttttc---aaacagaacatttactgactgctctcactttgatatttcagATCCATTCGAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTTGCTCGGTCCACAGATGATTTCAATGGAGCTCAACTGAAGGCTGTTTGTG
upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 8
gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaacaatctttattttatgtggtcttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
|| | ||||| | | | | || || |||| ||||||| | | |||| | || ||||||||||| | ||||||||||| |||| ||||||||||||||||| || || || || || || || ||||||| |||||||| || || || ||||
-----------------------------------------------gtttggt-atcttcaaattttatttgctgacattttttctctgacagaact---tttgcttatgtttttcacattaatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG
upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 8
gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaacaatctttattttatgtggtcttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
| || |||| | | | | | |||||| || ||| || || | | || | | | ||||| |||||||| || |||||||| |||| ||||||||||||||||| | || || || || || || |||||||| |||||||||||||| || ||||
------------------------------------------------gtttgttgtcttccaaactttacctgctgacacattgttcaatcaaaacatttactgactaccctcactttgat---attttagATTCATTCAAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTTGCCCGGTCCACAGATGATTTCAATGGCGCACAACTGAAGGCTGTCTGTG
upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 8
gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaa-ataaaataaatccttgttctgccagaactaaaacaatctttattttatgtggtcttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
|| || ||| ||| || | || | || | | | | | |||| || | || | || | | || || | |||||||| || ||||| |||| ||| | || |||||||| |||||||| |||| ||||| || || || |||||||| ||||||||||| || |||||||
--------------------------------------gtatgtcttcaatgaatattttcttctagatcattacacattgatcactctttgcagagctcttattgactct--ttcacattgtatt--tgtagATCCACTCGAGAAAGATGACTGTTCATCCGGATGTCAATTTTGAAGAACTGGCTCGATCCACAGATGATTTCAATGGGGCACAACTGAAAGCTGTTTGTG
upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------gtatgtctcctgaaatc-tgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaacaatctttattttatgtggtcttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
| | | | || || ||| || || |||| || || | || | | | || | ||| | | | | || | | | ||| |||| ||||| || ||||||||| ||| ||||||||||||||||| |||||||| || || || || ||||| || || || ||| ||||||| || |||
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA
upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S218_133V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgatt-atctttctttaaaaata------aaataaatccttgttctgccagaactaaaacaatctttattttatgtggtcttac-tctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
| || | | || | | | | || || |||| | ||| || ||| |||| ||| ||| | | | || || | | | ||||| | | ||| | | || || |||| |||||||| |||||||||||| ||||||||||||||| |||||||| || || ||||||||||| || || || ||| | ||||| || ||
gttcggataaacaatagcgcttggtagactttgaagtttgcataatcctgtacccctaacctaaccatgt-tttcacctattgttttactgtttgatccttctataattataccacctatacagatttttatgagcaggatatcttatcaatcactgt--aatgaactttcacctccagATTCATTCAAGGAAAATGAATGTACGGGGTGATGTCAACTTTGAGGAGTTGGCCCGTTCCACGGACGACTTTAACGGAGCCCAATTAAAGGCTGTATGCA
upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaaca-atctttattttatgtggtcttactc-tagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
| ||||| || ||| | || || || | || | | || |||| || || || ||||||| ||| | | | ||||| |||||||| ||| |||| || || |||||||||||||||||||| ||||| |||||||| || |
--------------------------------------------------------------------------------gttcgttcttcctcgtctagactgtattttgatcgaaagtcttttcgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG
upper sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaaca-atctttattttatgtggtcttactc-tagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
| ||||| || ||| | || || || | || | || || |||| || || || ||||||| ||| | | | ||||| |||||||| ||| |||| || || |||||||||||||||||||| ||||| |||||||| || |
--------------------------------------------------------------------------------gttcgttcttcctcgtctagactgtattttgatcgaaagtatttttgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCGMapped 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|29613635|gb|CB618648.1|CB618648EST: AAATTGAGTTCCNTCATCCATCCGAAGAAGCACGAGCTAGAATTTTGCAA ATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTG
genomic: AAATTGAGTTCCCTCATCCATCCGAAGAAGCACGAGCTAGAATTTTGCAAgtatgtctcc ... cttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTG
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:
64 (upstream exon),
75 (downstream exon)
Score:
23CGCGGACATTCTTGATCCTGCTTTGATGAGGTCTGGTAGGCTGGACCGAAAAATTGAGTTCCCTCATCCATCCGAAGAAGCACGAGCTAGAATTTTGCAAgtatgtctcc ... cttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatccttgttctgccagaactaaaacaatctttattttatgtggtcttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
tcttactct CT-rich tract
aactaaaacaatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaacaatctttattttatgtggtcttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG