Sequence
atgc intronic sequence ATGC exonic sequence...tcatatataaagttatagataatatttgcatcaattagagaaaacctgaatttcttctgttggactgaaaattcattgccttttattttttgcaatatagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGTCCTGAGTTCTCACTTGATGCAAAAAATTCAAAGGACACTGTTGCTGCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g56234.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g56234.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152319_T01 (Zea mays), 3'ss of exon 4
tcatatataaagttatagataatatttgcatcaattagagaaaacctgaatttcttctgttggactgaaaattcattgccttttatttttt----gcaatatagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGTCCTGAGTTCTCACTTGATGCAAAAAATTCAAAGGACACTGTTGCTGCTA
|| | | | ||| ||| | || | || ||| | | ||| || | | || | || | | || || ||| || ||| ||||||| ||||| || |||||||||||||||||||||||||| || | |||||| ||||||||||||||||||||| || ||||| || |||||||||
tcttttcttgcaatattagcc-tatct-tatta--tattgaagttttaattttgttgtatatgaatctaatgtaaaaagattcaatgctttatgtgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGACGCATGAAGAAGCTATTGGGTCCTAGGTTCTCACTTGATGCAAAAAACTCCAAGGATACCATTGCTGCTA
upper sequence: LOC_Os03g56234.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G085427_T02 (Zea mays), 3'ss of exon 4
tcatatataaagttatag-ataatatttgcatcaattagagaaaacctgaatttcttctgt-tggactgaaaattcattgccttttattttt---tgcaatatagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGTCCTGAGTTCTCACTTGATGCAAAAAATTCAAAGGACACTGTTGCTGCTA
| ||| || | || || || | ||| ||| | | | | || | | | | || || | || || ||| ||| ||| ||||||| ||||| || |||||||||||||| ||||||||||| || || |||||| ||||||||||||||||||||| || ||||| || |||||||||
----gtttaatcttttcttgcaacgttagcctaccttatt-aaagtttaattctgttgtatatcaatctaatataaaatgatttaatgctttatgtgccatacagGTCAGGCATTACTATTATCGTCTTGTTCGGCGCATGAAGAAGCTACTGGGTCCTAGGTTCTCACTTGATGCAAAAAACTCCAAGGATACCATTGCTGCTA
upper sequence: LOC_Os03g56234.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G05420.1 (Glycine max), 3'ss of exon 4
tcatatataaagttatagataatatttgcatcaattagagaaaacctgaatttcttctgttggactgaaaattcattgccttttattttttgcaatatagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGTCCTGAGTTCTCACTTGATGCAAAAAATTCAAAGGACACTGTTGCTGCTA
||| | ||| | | |||| ||| || | | | ||| || || ||| | | || || || | || | ||||||| ||||||||||| || ||||| |||| ||||| |||||||||||||| | || | | ||||| ||||| || || || ||| |||||| |
----gtatcca-ttacaactcccatttattgcaaata---atatcatgacttgttttagttttctt--acgtttttttccgggtgggggctgacttgcagGTCAGGCATTATTACTACCGACTTGTGAGACGGATGAACAAACTTCTTGGTCCAGGATTATGTTTGGATGCCAAAAACTCTAAAGATACTAATGCTGCAA
upper sequence: LOC_Os03g56234.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G23840.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------tcatatataaagttatagataatatttgcatcaattagagaaaacctgaatttcttctgttggactgaaaattcattgccttttatttt--ttgcaatatagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGTCCTGAGTTCTCACTTGATGCAAAAAATTCAAAGGACACTGTTGCTGCTA
| | ||| || || ||| | ||| | | || | | | |||| | || | | | || | || | | || | ||||||| ||||||||||| || ||||| |||| ||||| |||||||||||||| | || | | ||||| ||||| || || || ||| |||||| |
gtatccactaaaacttcacgtggctttttaaccctttgcattttcccattcatccacacccccccccccccccaaaaaaaaatgattatgttttagttttattgcaaataatatca-tgtcttgttttagttttcttacgcacttttttgtgtgggggctgacttgcagGTCAGGCATTATTACTACCGACTTGTGAGACGGATGAACAAACTTCTTGGTCCAGGATTATGTTTGGATGCCAAAAACTCTAAAGATACTAATGCTGCAAMapped 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|88357304|gb|CI622153.1|CI622153EST: AATTTTGAGAAGATCACGCTCCGTGTCCAGAGCAAAAACAAGGATCAG GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGT
genomic: AATTTTGAGAAGATCACGCTCCGTGTCCAGAGCAAAAACAAGGATCAGgtacaccatt ... tgcaatatagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGT
EST:
gi|88369569|gb|CI582764.1|CI582764EST: AATTTTGAGAAGATCACGCTCCGTGTCCAGAGCAAAAACAAGGATCAG GTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGT
genomic: AATTTTGAGAAGATCACGCTCCGTGTCCAGAGCAAAAACAAGGATCAGgtacaccatt ... tgcaatatagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgaatttcttctgttggactgaaaattcattgccttttattttttgcaatatagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGTCCTGAGTTCTCACTTGATGCAAAAAATTCAAAGGACACTGTTGCTGCTA
ttgccttttatttttt CT-rich tract
ttttattttttgcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatatataaagttatagataatatttgcatcaattagagaaaacctgaatttcttctgttggactgaaaattcattgccttttattttttgcaatatagGTCAGACATTATTACTATCGTCTTGTTCGACGCATGAAGAAACTTCTTGGTCCTGAGTTCTCACTTGATGCAAAAAATTCAAAGGACACTGTTGCTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - tgcatca
- - - - - - - - - - - - - - - - - -tagagaaa
- - - - - - - - - - - - - - - - - - - - - -acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttgg