Sequence
atgc intronic sequence ATGC exonic sequence...aaccaaaaatgaagtcctatccaattgacgcatagcacattatttcatgaatggcatataaagacctacctaaatattttcttgcttcaactgtttgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCACTAGAGACACTAAAGCGTGTTGTTGGTGCTGGCAATCGGGCTAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g42439.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G049288_T01 (Zea mays), 3'ss of exon 18
aaccaaaaatgaagtccta-tccaattgacg-catagcacattatttcatgaatggcatataaag-acctacctaaatattttcttgcttcaactgtt-tgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCACTAGAGACACTAAAGCGTGTTGTTGGTGCTGGCAATCGGGCTAGAG
| ||||| |||| | || | ||||||||||| | ||| | |||||| ||| | | | | | | | |||| |||||| ||||| ||||||| | ||| |||||||||||||||||||||||||||||||||||||||||||| | |||||| |||||||||| || |||||||| ||||||||| | |
----catcctgaagacctagtatgatcaatttcatagcacattctgtcacaagtggcatctaagggatccatcatattttttttttgcttgaactgccatgcagGTCATACCACTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCATTGGAGACATTAAAGCGTGTAGTCGGTGCTGGTAATCGGGCTCGTG
upper sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 12
aaccaaaaatgaagtcctatccaattgacgcatagcacattatttcatgaatggcatataaagacctacctaaatattttcttgcttcaactgtt-tgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCACTAGAGACACTAAAGCGTGTTGTTGGTGCTGGCAATCGGGCTAGAG
|| ||| || ||| | || | ||||||| ||| | ||| | ||| || ||| |||| | | || ||| |||||| |||||| | |||||||| ||| |||||||||||||||||||||||||||||||||||||||||||| | |||||| |||||||||| ||||||||||| ||||||||| | |
cactttaaa-aaaatccagtatgatcaattcatagcatattctgtcacaagtggaatctaaggacccatcataaccatttattgcttgaactgtcatacagGTTGTACCACTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCATTGGAGACATTAAAGCGTGTAGTTGGTGCTGGTAATCGGGCTCGTG
upper sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 18
-aaccaaaaatgaagtcctatccaattgacgcatagcacattatttc-atgaatggcatataaagacctacctaaatattttcttgcttcaactgtttgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCACTAGAGACACTAAAGCGTGTTGTTGGTGCTGGCAATCGGGCTAGAG
| | | ||| | | | | | || ||| || | | ||||| | || | | | | | | || || || |||||||||||| |||| |||||||| || || |||||||||||||| || | || || ||||| ||||| |||||||| | ||| || || || || || |
ctagtttctttttgataatatt-agtatgcttttgttgctgtacttccattatttatatatata-acttgcattgacctaatttttaaatttcttcttccagGTTGTTCCACTGCTAATGAAAGCTATAGGGTGGCAAGGTGGAAGCATTTTAGCTCTTGAGACTCTAAAACGTGTTGTGGTTGCAGGAAACCGAGCCAGGG
upper sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AT2G26890.1 (Arabidopsis thaliana), 3'ss of exon 18
aaccaaaaatgaagtcctatccaattgacgcatagcacattatttcatgaatggcatataa-----agacctacctaaa-----tattttcttgcttcaactgtttg-----cagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCACTAGAGACACTAAAGCGTGTTGTTGGTGCTGGCAATCGGGCTAGAG
| | | | | || ||| | | ||| | || | ||||| | || | |||||| ||| | ||| | || || ||||| |||||| | || ||||||||||| ||||||| |||||||| || | ||||| |||||||| ||||||||||||| |||||| |||||||| ||||
gttctctactctatttctctcctcctactctaccacacgctgtt--aaaaatggaaactagttgttggtgttacctatgacatgtataatgactcttaagttgattaaacaccagGTGGTTCCACTTCTCATGAAAGCAATAGGATGGCTTGGTGGAAGCATTTTAGCACTCGAGACACTTAAGCGTGTTGTTGTTGCTGGAAATCGGGCCAGAG
upper sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 18
aaccaaaaatgaagtcctatccaattgacgcatagcacattatttcatgaatggcatataaagacc---tacctaaatatt--ttcttgctt-caactgtttgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCACTAGAGACACTAAAGCGTGTTGTTGGTGCTGGCAATCGGGCTAGAG
|| | || | | | | | || | ||| | | | | || | | |||| | | || ||| | ||| | |||| | || || |||||||| ||| | | |||||||| || ||||||||||||||||| ||||| || || || ||||| || |||||||| | |||||| ||||| ||||| |
---catagttgcatt--tggcaacttcagacat-gtgtagtgctctgtgtttatcttatatataatcggtatctagagattcatgcttgttggtctttgcttccagGTTGTACCACTCTTAATGAAAGCTATCGGATGGCAAGGTGGAAGCATACTAGCTCTTGAAACACTGAAACGTGTTGTGGTTGCTGGAAATCGAGCTAGGGMapped 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|33683077|gb|CF311316.1|CF311316EST: GCACTACTTGTGTAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAG GTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGGTGGAAGTATACT
genomic: GCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAGgtattgaatt ... ctgtttgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGG-TGGAAGTATACT
EST:
gi|2428708|gb|C73171.1|C73171EST: GCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAG GTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAG-TGGAAGTAT
genomic: GCACTACTTGTGCAGAAGCTATGGCAGCCACAAGTGCAGGAACTCCTCAGgtattgaatt ... ctgtttgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgaatggcatataaagacctacctaaatattttcttgcttcaactgtttgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCACTAGAGACACTAAAGCGTGTTGTTGGTGCTGGCAATCGGGCTAGAG
acctaaa putative branch site (score: 3)
taaatattttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaccaaaaatgaagtcctatccaattgacgcatagcacattatttcatgaatggcatataaagacctacctaaatattttcttgcttcaactgtttgcagGTTGTTCCATTGCTTATGAAAGCAATTGGATGGCAAGGTGGAAGTATACTGGCACTAGAGACACTAAAGCGTGTTGTTGGTGCTGGCAATCGGGCTAGAG
-accaaaa
- - - - - - - - - - - - -tgacgca
- - - - - - - - - - - - - - - - - gcacatt
- - - - - - - - - - - - - - - - - - - - - - - atgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctacct