Sequence
atgc intronic sequence ATGC exonic sequence...tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os10g28320.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G813143_T02 (Zea mays), 3'ss of exon 4
-tgttagctcctattcaagtttgtgcatcattt-----actccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
|| || || ||| | || ||| |||||| | | |||| |||||| || | ||| | || | | | || | |||| |||||||||||||| |||||||| ||||||||||||||| |||||||||||||||||||||||||||| |||||| | | | ||||| || ||| ||
ttgcaagttctaatt--aacttatgcttcatttttcttatctttggttcgttgaacatcgatatca-tgcatttatctgtttgtcataaa---tgcttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG---
upper sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G40860.1 (Glycine max), 3'ss of exon 4
--------------------tgttagctcctattcaagtttgtgca-------tcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
||||| | || || | | | | |||| | ||||| || | | | | | | | || | || | || | ||| |||||||| ||||| ||||||||||| |||||||| || |||| |||||||| |||| |||| | | ||| | | | || | | || | |||
gttagttcaagttcatggcactgcagctcttcttgaaaggagggaaaagaaagtggtttagttgttgttggctgtatttttgtgttaatgcgactt--caattttttaatgcttatattggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTG---
upper sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G27130.1 (Glycine max), 3'ss of exon 5
tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
| | ||| || | | || | | | | | || ||| |||| || | | |||||||||||||||||||||||| ||||||||||| |||| || ||||| ||||
------------------------gttaaattaagagaaattaaattaaattaaaatgcacgttact----tactttggtaaagctttttattgatacagGGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTG-----------------------------------------------
upper sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G40860.4 (Glycine max), 3'ss of exon 4
--------------------tgttagctcctattcaagtttgtgca-------tcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
||||| | || || | | | | |||| | ||||| || | | | | | | | || | || | || | ||| |||||||| ||||| ||||||||||| |||||||| || |||| |||||||| |||| |||| | | ||| | | | || | | || | ||||||
gttagttcaagttcatggcactgcagctcttcttgaaaggagggaaaagaaagtggtttagttgttgttggctgtatttttgtgttaatgcgactt--caattttttaatgcttatattggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGGTA
upper sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G43360.1 (Glycine max), 3'ss of exon 4
tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgcc-actcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
||| || | | || | ||| | | | || | | ||| | | ||| |||| || | | |||||||||||||||||||||||| ||||||||||| |||| || ||||| |||| ||||| | | | | | | | || | | || | |||
-tttaatcactggctacatgtgaaaagaggttaaattaagagaaataaaataaaattaaaatgcacgttacttactttggtaaagctttttattgatacagGGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAACTGTGTCAACAGTTAGCTCCCTG---
upper sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G40880.4 (Glycine max), 3'ss of exon 5
tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
| | | || | | || || | |||| | || || || | || |||||||||||||||||||| ||||||||||| |||| || ||||| |||| ||||| | | | | | | || || | || | | |
----------------------------aaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagctt--ttattgatagagagcttggcattggaattgtaccatatagCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCC-TGCAAGTACAGTCCTG--
upper sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G40880.3 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------------------tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgccac-------tcattcgaagcattacttgtgtt--cagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
| | ||| | ||| || | | | | | |||| | | || || || ||| | | ||| | || || |||||||||||||||||||| ||||||||||| |||| || ||||| |||| ||||| | | | | | | || || | || | | |
gtcagttcaacttccccaaattcatagtaatgtacagctctcataactattttttcactaataaataaataatttgaatttctgtttaattatgagccacatgaaaagagggtagaaaaataagactaaaaaaattggttagctagattttttgtttatgttttaatgagatcactttgttaaaagcttttattgatagAGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCC-TGCAAGTACAGTCCTG--
upper sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0030g01960.t01 (Vitis vinifera), 3'ss of exon 4
----------tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
|| | | | | ||| || || | | | ||| | | || | | | || | | | || | ||| || | | ||||||||||||||||||||| |||||||| | || |||| ||||| || |||| ||| |||| | ||| | || | || | | | |||
aaggattatatgcttgatacctttcttgtatggctacaactctctctctctctcttaattataaatatgacatgctgttttcatttatttaaa----------tatgcagGGAGCTTGGCATTGGAATAGTTCCATACTGTCCTCTTGGTCGTGGATTTTTTGGTGGTAGGGGAGTTGTGGAAAGTTTGCCTGC--ATACTTG-------Mapped 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|29661845|gb|CB658120.1|CB658120EST: TGGTCTCTATGGACCAGGGATATAGAGGAAGAAATAATCCCGCTGTGCAG GGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTT
genomic: TGGTCTCTATGGACCAGGGATATAGAGGAAGAAATAATCCCGCTGTGCAGgttcatgtac ... ttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTT
EST:
gi|29687719|gb|CB683994.1|CB683994EST: TGGTCTCTATGGACCAGGGATATAGAGGAAGAAATAATCCCGCTGTGCAG GGAGCTTGGCATTGGAATTGTTCCATATAGGCCAATTGGCCGTGGCTTCTT
genomic: TGGTCTCTATGGACCAGGGATATAGAGGAAGAAATAATCCCGCTGTGCAGgttcatgtac ... ttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
attactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttagctcctattcaagtttgtgcatcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - agctcct
- - - - - - - - - - -gtgcatc
- - - - - - - - - - - - - - - - -ctccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgtgcc