Sequence
atgc intronic sequence ATGC exonic sequence...ttagacatgtggatgcttgctcctagtgtgaatgctactttatgtttttcttaaaagaagttattatatggcctttcttcacatattttcttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g49230.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g49230.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G167560_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------------------ttagacatgtggatg-cttgctcctagtgtgaatgctactttatgtttttcttaaaagaagttattatatggcctttcttcacatattttcttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC
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gtaagcacgtttaaatgtctgcttgaggttgttctgcgcttaacattcatagatcgtggctatctttttaaggcaaaaaaatgtctccaaccttctgtgtctcttgtttctagtttcgataatgc---attttccttgcagaagtcgctgattcacctttccttttcacgaatttgg---tcgacagGTTTGACAAGAAGATCAGATATGCTTCTCGCAAGGCTAGGGCAGACGTGAGGAAGAGGGTCAAGGGACGGTTTATAAAGGCTGGCGAAGCGTATGACTAT
upper sequence: LOC_Os02g49230.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G075562_T02 (Zea mays), 3'ss of exon 3
-------------------------------------------------ttagacatgtggatgcttgctcctagtgtgaatgct----actttatgtttttcttaaaagaagttattatatggcctt--tcttcacatattttcttc----------ttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC
| | | | ||| || | | ||||| || || || | ||| |||| ||| | || ||| | | | || | | |||| |||||||||||||| || ||||||||||| ||||||||||| || ||||| || ||||||| |||||||| ||||||| || ||||| || |||||
gtaagcacggctaaatgtctttttgtggttatttttctgcgcctaacattcatatagaccatggctatctttttaagcaaatgcctcccaccttctgggtctctcgtttctagttccaatactgtattgaccttttcttttcttttccacgaatttggccgacagGTTTGACAAGAAGATCAGATATGCTTCTCGCAAGGCTAGGGCGGACGTGAGGAAGCGGGTCAAGGGACGGTTCATAAAGGCCGGTGAAGCGTACGACTAT
upper sequence: LOC_Os02g49230.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0194g00070.t01 (Vitis vinifera), 3'ss of exon 4
--ttagacatgtggatgcttgctcctagtgtgaatgctactttatgtttttcttaaaagaagttattatatggcctttcttcacatattttcttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC
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actaaaataagggtaggatttttatggaatttgattagaatgaaaattttcataactaaaaaataattttttttcttt-ttcat-caatgacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTACMapped 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|700150|gb|D46441.1|D46441EST: AGCAGAGATAATGCTCTTACACGGTACAAGGAGAAGAAGAAGAGAAGNAA ATTTGACAAGNAGGTAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAG
genomic: AGCAGAGATAATGCTCTTACACGGTACAAGGAGAAGAAGAAGAGAAGAAAgtaagtgcat ... ttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAG
EST:
gi|33815340|gb|CF333525.1|CF333525EST: AGCAGAGATAATGCTCTTACACGGTACAAGGAGGAGAAGAAGAGAAGAAA ATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAG
genomic: AGCAGAGATAATGCTCTTACACGGTACAAGGAGAAGAAGAAGAGAAGAAAgtaagtgcat ... ttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcttaaaagaagttattatatggcctttcttcacatattttcttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC
cctttcttcacatatt CT-rich tract
ttaaaagaagttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagacatgtggatgcttgctcctagtgtgaatgctactttatgtttttcttaaaagaagttattatatggcctttcttcacatattttcttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC
- - -catgtgg
- - - - - - -tgcttgc
- - - - - - - - - - - - - - tgaatgc
- - - - - - - - - - - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa