Sequence
atgc intronic sequence ATGC exonic sequencegtaagtacagggcttcctatattcagattgcaatgtatttccccatacttttctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g14260.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 7
----gtaagtacagggcttcctat-att--cagattgcaatgtatttccccatacttttctttgatgtatttatagtatataggcagtatatgattgtgtttcccttt---ctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
| || ||| || ||| ||| | |||||||||| ||| | | || | || | | | ||||| |||| |||||| | ||| ||| |||||||||||| ||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||||||| || |||||||||||||| ||||| |||||
gtaaggaatctgaggctttattatcattactacattgcaatgtgtttttttacatttctgttcggtct----------tatagacagtgcatgattttttttttttttgccctcttgtagGCATTACAATATGAACCGCATCAGACTTGTTTGGTCAAGTATATGGCATGTCTTGTCTGATTTTTTTGTCACCATTGGCTGCTCAGAAAATCTTTCAATC
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 7
gtaagtacagggcttcctatattcagattgcaatgtatttccccatacttt-tctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
||| || | |||| | | || | || | || ||||| || | || ||| | | || || || | | |||||||| |||||||| |||||||||||||| ||||||||||| |||||||| | |||||||| ||||| || |||||||| | | || || ||||||
------acaaatgtt----tgggcagagcatcaagcatatgattatgttgcatcattgattgatgttta-tatgctgctacctattgtctgacacgattattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTTGGCAAACCTTTCAATT
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 7
gtaagtacagggcttcctatattcagattgca-atgtatttccccatacttttctttgatgtatttatagtatataggcagtatatgattgtgtttccct----ttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
| || || | | || | || | || |||| || || || |||| || | |||| | ||| || | | |||||||| |||||||| |||||||||||||| ||||||||||| |||||||| | |||||||||||||| || |||||||| || | || || ||||||
--------------ccaaatgtttgggcagagcatcaagcatatgattatgttgcatgattggttgat-gtttatatgctgctatctgttgtttgacccgattattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTTTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 8
gtaagtacagggcttcctatattcagattgcaatgtatttccccatacttt-tctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
||| || | |||| | | || | || | | ||||| || | || ||| | || ||| | || | | |||||||| |||||||| |||||||||||||| ||||||||||| |||||||| | |||||||| ||||| || |||||||| || | || || ||||||
------acaaatgtt----tgggcagagcatcaagcatatgattatgttgcatgattgattgatgttta-tatgctactacctgttgtttgactcgaatattatgtaacagGCACTATAATATGAACCGCATCAGGCTTGTGTGGTCAAGCATCTGGCATGTTCTCTCTGATTTCTTTGTAACTATTGGCTGTTCGGCAAACCTTTCAATT
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 7
gtaagtacagggcttcctatattcagatt-gcaatgtatttccccatacttttctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
|| | || || || || |||| || || ||| | || || || ||||| | | | | |||| | ||| | |||||||| |||||||| |||||||||||||| ||||||||||| |||||||| | |||||||| ||||| || |||||||| || | || || ||||||
--gagcattaggtttatgattttgtgattcgcgattaattaatctttatacactgctgccttagttatattgtttgactttgaggggattat---------tctgtaacagGCACTATAATATGAACCGCATCAGGCTTGTATGGTCAAGCATTTGGCATGTTCTCTCTGATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATT
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G45360.1 (Glycine max), 3'ss of exon 9
gtaagtacagggcttcctatattcagattgcaatgtatttccccatacttttctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT-----------------------------------------------------------
|| || | || | ||| | | |||| | |||||||| |||||||| |||||||||||||| |||||||||||||||||||| | || ||||| ||||| || |||||||| || | || || ||||||
---------------------------------------------------------------------taattatactgtttgactttgaggtgattattctgtaacaggcactataatatgaaccgcatcaggcttgtgtggtcaagcatatggcatgttctctcagATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATTGCAATTTTTGCAATGGATTCCTTGCGTCAGTTGTCAATGAAATTTCTGGAGCGGGAGGA
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------gtaagtacagggcttcctatattcagat-tgcaatgtatttccc-catacttttctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
|| | | || || | || || | | ||| | | || | | | | | || ||||| ||| | | | | || ||||| | || | | ||||| || || ||||||||||| |||||||| ||||||||||| ||||| || | || | ||| ||||| || ||||| |||||||||||||| || |||
gtaagaatctcctagtttcgttcctctctgttctctcatatactgcatataagagacgttctctgttcttagcaactttaagtatgtagtctg-acaattttctgtttgtcatt-tgtgacagGCATTATAACATGAATCGCATAAGGCTTGTTTGGTCAAGCATCTGGCAAGTGCTATCAGGTTTCTTTGTGACCATTGGATGCTCAGAGAATCTTTCTATT
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagtacagggcttcctatattcagattgcaatgtatttccccatacttttctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
| ||| | | || | ||| | | || | | | | | | | | ||| | ||||| || | | |||||||| || ||||| ||||| || ||||||||||| ||||| |||||||| | |||||||| ||||| || |||||||| || || || ||||| |||
--------------------gtaaggatcaatcttttctttacgatatctgttttgtttttgctcactctctct----tatttat-accctgtttg--ttgtaatggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 7
---------------------gtaagtacagggcttcctatattcagattgcaatgtatttccc-catacttttctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
|| || | || ||| | | | |||| || ||| | | || ||| | | | | | | | || || | | | |||||||| || ||||| || ||||||||||| ||||||||||| |||||||| | || ||||| ||||| || |||||||| |||||||| || ||||||
gtatgaatcattctcaatttgtcttgttcatgttttagcataccatattagtgcttcatttattatttatatttgtcagctgctattaaaaattttgctaaaattctaagtgatttgttttcttttacacagGCACTATAACATGAACCGTATCAGGCTTGTGTGGTCAAGCATCTGGCATGTACTCTCAGATTTCTTTGTAACCATTGGCTGTTCAGAGAACCTTTCAATTMapped 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|29628227|gb|CB633238.1|CB633238EST: CAAAGATTGTTGAGATTGC GCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGT
genomic: CAAAGATTGTTGAGATTGCgtaagtacag ... tctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
ctttgat putative branch site (score: 5)
ttgtgtttccctttct putative PPT
tatttatagtatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtacagggcttcctatattcagattgcaatgtatttccccatacttttctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT