Sequence
atgc intronic sequence ATGC exonic sequence...tgttggactgcaatgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattgtttgtttacttgctcctttgttttcgattgcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g46720.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 2
--tgttggactgcaatgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattgtttgtttacttgctcctttgtt-ttcgatt----gcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
| || |||| | | | | ||| | | | | | || || | | | | || | ||| | | || | | |||| ||| | || ||||||||||| || || || ||||| ||||| || |||||||||||||| ||||| ||||| |||||||| || |||||||| |||||||
gttagtgtttcctcatgcctccttttgtgtttctgtatccaggacacctgtatcttatttatatcactaatttatatattgtttttgtgctgcttgatttttcacagTCTGGAGATTTGGAAAAGGCACAACTTGGTCTGGGACATAGTTACAGCAGGGCAAAGGTGAAGTTTAATGTTAACCGTGTAGACAACATGGTTATTCAAG
upper sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 2
-----------tgttggactgcaatgctttgatgctttcatatgttcc---ttgcataaaatggtttttttcctgttattgtttgtttacttgctcctttgttttcgattg-------cagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
| || || ||| || | || ||| ||| | | ||| | |||||| || |||| | | ||| | | ||||| || | || ||||||||||| || || || ||||||||||| || ||||| |||||||| || |||||||| |||||||| || |||||||| |||||||
gttagcatttactcctgcctcgtgtgtttttgcagaagcagaatcaccgtgttgtataggaatatatttcgcaagttatt--ttatttaaattattttttttccttgattgaattctgtagTCCGGGGATTTGGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAATTCAATGTTAACCGTGTTGACAACATGGTCATTCAAG
upper sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 2
--tgttggactgcaatgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattg-tttgtttacttgctcctt-tgtt-ttcgatt---gcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
| || |||| | | | | ||| | |||| || | || | | | | ||| | || | | || || | | |||| ||| | || || |||||||| || || || ||||||||||| || ||||| |||||||| ||||| ||||| |||||||| || |||||||| |||||||
gttagtgtttcctcatgcctctttttgtgtttctgtgtgcaggataactgtgtcctatttttatcactaatttatatatatattttttatgctgcttgattttcacagTCTGGAGATTTAGAAAAGGCACAACTTGGTCTGGGGCATAGTTACAGCAGAGCAAAGGTGAAGTTTAATGTTAACCGTGTTGACAACATGGTTATTCAAG
upper sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 2
tgttggactgcaatgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattgtttgtttacttgctcctttgttttcgattgcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
| || ||| || | | | ||| | | | || | || | | || | |||| | | || | | || | |||| ||| | ||||| ||||||| || | | || ||||| ||||| || ||||| ||||||||||| ||||| |||||||||||||| |||||||
----gtgtgatctcctttctatgtgtttaaaatctttttgtctg--tttgcttatctcatatggtt-tgtgttctcataaaaaatttctgtttat-gtagCCTGGTGATCTTGAAAAATCTCAGCTTGGATTAGCTCACAGCTACAGCAGAGCCAAGGTGAAGTTCAATGTTAACCGAGTGGATAACATGGTTATTCAAG
upper sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 2
tgttggactgcaatgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattgtttgtttacttgctcctttgttttcgattgcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
|| ||| | || || | ||| | | | | || | || || | || | | ||| | || |||| ||| |||||||| ||||| || || || | |||||||| ||||| |||||||| ||||||||||| ||||| |||||||||||||| |||||||
------------------gtgtgttttttatttttgattacctaatacc-tacacatatttttgctattcgtgctcaatatcatcttctttataatgtagCCTGGTGATTTGGAAAAAGCTCAACTTGGACTAGCTCATAGCTACAGCAGAGCAAAGGTGAAGTTCAATGTTAACCGGGTGGATAACATGGTTATTCAAG
upper sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 2
--------------tgttggactgcaa----tgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattgtttgtttacttgct--cctttgttttcgattgcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
| || | ||| ||||| ||| | | || | || ||| ||| | || || ||| | | ||| |||| ||| |||| ||| | |||||||| || || || ||||| || || || ||||| |||||||| ||||||||||||||| | || ||||| ||||| ||||| |
gtttgctttatttattttttccctcaaaatatgcttctgcctttttgtgtattacaacaattaaagggtaggcggtattttctttgcaatttctcttatagtatttatttttccttgtagCCTGGAGACCTAGAAAAGGCCCAACTTGGTCTGGGACACAGTTACAGCAGAGCAAAGGTGAAGTTCAATGTGAACAGAGTCGATAATATGGTCATTCAGGMapped 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|58689280|gb|CK077967.1|CK077967EST: TGCTCCGCGGAGTGCGGCTACACTTCGATCATTTCATTGATCAACTCAAG CCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGG
genomic: TGCTCCGCGGAGTGCGGCTACACTTCGATCATTTCATTGATCAACTCAAGgttgttgatt ... tcgattgcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatggtttttttcctgttattgtttgtttacttgctcctttgttttcgattgcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
tttacttgctcctttg CT-rich tract
ttattgtttgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttggactgcaatgctttgatgctttcatatgttccttgcataaaatggtttttttcctgttattgtttgtttacttgctcctttgttttcgattgcagCCAACTGACTTGGAAAAGGCTCAGCTAGGCCTGGGGCATAGCTATAGCAGGGCAAAGGTTAAGTTCAATGTGAACCGTGTGGATAACATGGTAATTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - -gactgca
- - - - - - - - - tgatgct
- - - - - - - - - - - - - -catatgt
- - - - - - - - - - - - - - - - - -ccttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacttgc