Sequence
atgc intronic sequence ATGC exonic sequence...gcgacagaataagagtgtcttacagctgattttacccacccaatattattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g26610.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 11
gcgacagaataagagtgtcttacagctgattttacccacccaatattattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
||||| | | || || | | |||| | ||| | | |||||||||||||| |||||||||| ||| | |||||| ||||| |||||| ||||||||||||| |||||||| ||||| ||||| ||||||||||||||||||||
--------gtaagattcttttctga---gttgcagttttaatgttctattttgtactattttattgattgccactaactaatccattgcgctggtgctagCATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 10
gcgacagaataagagtg--tcttacagctgattttacccacccaatattattcgatgctactgca-gtgattgccactaacaaatccattgctctgatact----agCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
| || | | || |||| || | | ||| | | | | || || || | || | ||| | | |||| | | |||| || || || || ||||| ||||| || ||||||||||||||||| || || |||||||| || |||||||
--------gtgaggctcatttttttagct-atctcag--acctagtttaacctcatacttctctgtatacttcctcttaattcttttcctcctcttgttttccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 10
-----gcgacagaataagagtgtcttacagctgattttacccacccaatattattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
|| | | | ||| | | || |||| | ||| ||| | || | | | | | | | | | ||| | | ||||| || || || || ||||| ||||| || ||||||||||||||||| || || |||||||| || |||||||
gtgaggctcattttttgggctatctcagacctagtttt-ctaacctcatacttctctgtatactttctcttaattcttttcct---cctcttgtttt--ccatagCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 11
------gcgacagaataagagtgtctt-acagctgat-tttacccacccaatattattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
| | || | | || | ||||| | |||| |||| || || ||| | | | || | ||| ||||| ||||| || || || || || ||||| || ||||| ||||| ||||||||||| |||||||| |||||||
gtatggtcttccttattcagttatgttcagagctgttgtttataagtccaacttt------tgtctggatagtatatttaatttgttcttcttgttttctttccatagCATCCAGGAACAACCATAGTCACGGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTGMapped 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|29613465|gb|CB618478.1|CB618478EST: TAAACCGTAACAGATTGATTGCTTTGATGTCTGCCATAGTTCTTGAAGAG CACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACT
genomic: TAAACCGTAACAGATTGATTGCTTTGATGTCTGCCATAGTTCTTGAAGAGgtaagatctc ... ctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
ttgctct CT-rich tract
taacaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcgacagaataagagtgtcttacagctgattttacccacccaatattattcgatgctactgcagtgattgccactaacaaatccattgctctgatactagCACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTG
- - -agaataag
- - - - - - - - - - - - gctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaaa