Sequence
atgc intronic sequence ATGC exonic sequence...caaaaatgtatattttcctacaattctcatcttcgaattgttaaagtagcttcatataacgctgttattgcttattaagcatgtactgttctgatcacagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g15360.7 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g15360.7 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G163473_T01 (Zea mays), 3'ss of exon 4
caaaaatgtatattttcctacaattctcatc--ttcgaattgttaaagtagctt-catataacgctgttattgctta---ttaagcatgtactgttctgatca--cagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA
|| | || ||| || || | ||| || | || || | | ||||| ||||| || ||| ||||| |||| || ||||| |||||||| || || ||||||||||||||| |||||| ||||||||||| |||||||||||| ||||||||||||||||||| ||||| | |||||
-------ttacgcgtggctgagatttatattaatttgcatt-ttgcaatattttgtttgtcacgctaaatgtgcttgacctttgacatatactgctctggtcttccagGATAGGGATCGCAAGCTGCGGATATTTTCTGGAATTGAGCATCCATTCCATGACCGCCCTCTTGAAGCTTTTGTGATGCCACCACGGCAAGTACGGGAGA
upper sequence: LOC_Os05g15360.7 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 5
caaaaatgtatattttcctacaattctcatcttcgaattgttaaagtagcttcatataacgctgttat-tgctta---ttaagcatgtactgttctgatca--cagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA
| ||| || || | |||| |||| | | | | | ||| | || ||||| || ||| ||||| |||| || ||||| |||||||| || ||||||||||||||||||| || || ||||||||||| |||||||| ||||||||||||||||| ||||| ||||| | ||||
-----tttcataacatcttattgta-tcatggtcgaggaatcatgccttttgctggtcacgttaaaatgtgcttggtgtttgacatatactgctctggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA
upper sequence: LOC_Os05g15360.7 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G22420.1 (Glycine max), 3'ss of exon 5
----caaaaatgtatattttcctacaattctcat-cttcgaattgttaaagtagcttcatataacgctgttattgcttattaagcatgtactgttc-tgatcacagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA
| | ||||| | | || | | | | | | || || | || | | ||| || ||| |||| || |||| || | ||||||||||||| ||||| ||||| ||| |||| | ||||||||| || ||||||||| |||||||||| ||||||||| || | || | || |
tcatttggttagaactttttctgatattttttgttccttataatattgaataactgatattgtaagttgtatttactt-----gcat-tattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCGTTTGTTGATCGCCCACTTGAACCTTATGTGATGCCTCCTAGAAGTGTACGAGAAA
upper sequence: LOC_Os05g15360.7 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G36450.1 (Glycine max), 3'ss of exon 5
-------caaaaatgtatattttcctacaattctcatcttcgaattgttaaagtagcttcatataacgctgttattgcttattaagcatgtactgttc-tgatcacagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA
| | | || | || || | || | | | || || || || ||| | | || || ||| |||| || |||| || | ||||||||||||| ||||| ||||| ||| |||| | ||||||||| || ||||||||| |||||||| | ||||||||| || | || | ||| |
ttcatttggttagagctttttctgatatttttttgttccttataatattgaa-taactg-atactaagttgcatttactt-----gcat-tattgttaatggatatagGACAGGGATCGAAAATTAAGGATCTTTCCTGGCAGTGAGCACCCTTTTGTTGATCGCCCACTTGAACCGTATGTGATGCCTCCTAGAAGCGTACGGGAAA
upper sequence: LOC_Os05g15360.7 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 4
caaaaatgtatattttcctacaattctcatcttcgaattgttaaagtagcttcatataacgctgttattgcttat-taagcatgtactgttctgatc--acagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA
| ||| | | | || | || ||||| | | | || | | | | ||| | | | | || || | |||||| || ||||| ||| | ||||||||| |||| |||||||||| ||| |||| | ||||||||||||| ||||||||| || || ||||| | || |
---ttttagtcattatatgaatgatgtcttgttaactttgtttagatgattcaatgtgtttgcttgttggtttacattacaacgccactttatgtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAAMapped 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|29683757|gb|CB680032.1|CB680032EST: TCTTTTCGTGAACTATAAGGATGGTTGTGACTTGCGAAGGGTCTTGCTTC GACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
genomic: TCTTTTCGTGAACTATAAGGATGGTTGTGACTTGCGAAGGGTCTTGCTTCgtatgtaccc ... ctgatcacagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
EST:
gi|86602141|gb|CI260611.1|CI260611EST: TCTTTTCGTGAACTATAAGGATGGTTGTGACTTGCGAAGGGTCTTGCTTC GACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
genomic: TCTTTTCGTGAACTATAAGGATGGTTGTGACTTGCGAAGGGTCTTGCTTCgtatgtaccc ... ctgatcacagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagcttcatataacgctgttattgcttattaagcatgtactgttctgatcacagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA
ttctgat putative branch site (score: 3)
ctgttct CT-rich tract
ttattgcttattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaaaatgtatattttcctacaattctcatcttcgaattgttaaagtagcttcatataacgctgttattgcttattaagcatgtactgttctgatcacagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA