Sequence
atgc intronic sequence ATGC exonic sequence...gaatgcattaacacagagctatgatcaccgcacaattttctatctcccctagtcacacatgtttgtgtgcgtttttcattgtgttttttcactctatcagCTTCCTTGATCCTGGACCACATGGAAGCGGAAGGTATTCTGTGGAAATGCTCCCTGAAATAGAACAGAGGGACTTCAGGAAGGGTGCCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g07880.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 5
gaatgcattaacacagagctatga-tcaccgcacaattttctatctcccctagtc---acacatgtttgtgtgcgtttttcattgtgtttt-ttcactctatcagCTTCCTTGATCCTGGACCACATGGAAGCGGAAGGTATTCTGTGGAAATGCTCCCTGAAATAGAACAGAGGGACTTCAGGAAGGGTGCCCAG
| | | | | || | ||| | || || |||| || | ||| | | | || | | ||| | | || | || |||||||||||| |||||||| |||||||||| ||||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||
-----ctaaagagtaaatcaataagtcatcccagttttatctaacttcattagctgaaatgaaaataggtccacatgtttattctgatcttgtccatgttatcagCTTCCTGGATCCTGGCCCACATGGAACTGGAAGGTATTCCATGGAAATGCTTCCTGAAATAGAACAGAGGGACTTCAGGAAGGGTGCCCAG
upper sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 5
gaatgcattaacacagagctatgatcaccgcacaatt----ttctatctcccctagtcacacatgtttgtgtgcgtttttcattgtgttttttcactctatcagCTTCCTTGATCCTGGACCACATGGAAGCGGAAGGTATTCTGTGGAAATGCTCCCTGAAATAGAACAGAGGGACTTCAGGAAGGGTGCCCAG
|| |||| ||| | || || ||||| | || | | || || || ||| || || || | |||||||| | |||||||| |||||||||| ||||||||| | |||||||||| |||||||||||||||||||||||||||||||||||||||
--gccttttgttctagagagtaattcaatgagttatcccagttttatctaacttaatta-actgaaatgaaaataagttcacatgt-ttattccatgttgtcagCTTCTTCGATCCTGGCCCACATGGAACTGGAAGGTATACGATGGAAATGCTTCCTGAAATAGAACAGAGGGACTTCAGGAAGGGTGCCCAGMapped 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|29662010|gb|CB658285.1|CB658285EST: GATTACATATATAATTTTTTGATGGGAACAAACGTCAGCTTCATTGATTG CTTCCTTGATCCTGGACCACATGGAAGCGGAAGGTATTCTGTGGAAATGCT
genomic: GATTACATATATAATTTTTTGATGGGAACAAACGTCAGCTTCATTGATTGgtaagagcgc ... actctatcagCTTCCTTGATCCTGGACCACATGGAAGCGGAAGGTATTCTGTGGAAATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccctagtcacacatgtttgtgtgcgtttttcattgtgttttttcactctatcagCTTCCTTGATCCTGGACCACATGGAAGCGGAAGGTATTCTGTGGAAATGCTCCCTGAAATAGAACAGAGGGACTTCAGGAAGGGTGCCCAG
ttttttcactctatc CT-rich tract
tttttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatgcattaacacagagctatgatcaccgcacaattttctatctcccctagtcacacatgtttgtgtgcgtttttcattgtgttttttcactctatcagCTTCCTTGATCCTGGACCACATGGAAGCGGAAGGTATTCTGTGGAAATGCTCCCTGAAATAGAACAGAGGGACTTCAGGAAGGGTGCCCAG
gaatgca
- - - - - acacaga
- - - - - - - - - - - - - -ccgcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtgtt