Sequence
atgc intronic sequence ATGC exonic sequencegtacgatccaccgacgattattgcattattggcatgttgagatgataatgcaaaagactttagaaccgatgcttctttttttttttttgcagCGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGGTGGAAGTGGCCATTTTGCGCAAACAGTGAAGGCTCTAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g43576.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g43576.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G42600.1 (Glycine max), 3'ss of exon 4
gtacgatccaccgacgattattgcattattggcatgt-tgagatgataatgcaaaagactttagaaccgatgcttctttttttt----------tttttgcagCGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGGTGGAAGTGGCCATTTTGCGCAAACAGTGAAGGCTCTAAAG
|| | || | | || || ||||| | | || || | ||| ||||| | || | | || ||||||||| || || ||| |||| || |||||||| ||| | ||||| || |||||||| ||||||||||||||||| || || || || ||| | |||
--acaagttacaatgcctagatttatcatgggcatatattgtgtgctacta-aaactttattagatctcattccctgctaattacaagctaccatttttgcagTGTGGA-TATATTGTCCTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG
upper sequence: LOC_Os05g43576.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G24430.1 (Glycine max), 3'ss of exon 2
-----gtacgatccaccgac-gattattgcattattggcatgttgagatgataatgcaaaagactttagaaccgatgcttctt---tttttttttttgcagCGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGGTGGAAGTGGCCATTTTGCGCAAACAGTGAAGGCTCTAAAG
||| || | || ||| || | ||| ||| | | | | | | ||| | | || | | | ||||||||||||| || ||| |||| | |||||||| ||| | ||||| || |||||||| ||||||||||||||||| || || || || ||| | |||
acaagttacaatgcctagattgatcatgggcatat-attttgtgctgctaaaactttattagatctcattccctgttaattacaagctaccttttttgcagCGTGGATTATATTGTCTTAACAAGTGTGGATCGTGATGATCTGCCTGATGGAGGAAGTGGCCATTTTGCTCAGACTGTCAAAGCTATGAAG
upper sequence: LOC_Os05g43576.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G08415.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------gtacgatccaccgacgattattgcattattggcatgttgagatgataatgcaaaagactttagaaccgatgcttctttttttttttttgcagCGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGGTGGAAGTGGCCATTTTGCGCAAACAGTGAAGGCTCTAAAG
|| || | || | | | | || |||| | | || ||| | | | | | || | | |||| ||| |||||| |||||||| | || | || || || || | || || | ||||||||||||||||| ||||||||||| || || || ||| | |||
gaaaattaaaaatagtgtctctcaacagtcactactgcatc--tttgtt-aatttatgatgggtgtatcatgatatgctattttgcattttcctttgttgcagTGTAGACTACATAGTTATTACCAGCGTAGACCGTGACGATATACCTGATGGTGGAAGTGGACATTTTGCGCAGACTGTCAAAGCTATGAAG
upper sequence: LOC_Os05g43576.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv10s0071g01020.t01 (Vitis vinifera), 3'ss of exon 2
---gtacgatccaccgacgat-tat-tgcattattggcatgttgagatgataatgcaaaagactttagaaccgatgc---ttctttttttttttttgcagCGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGGTGGAAGTGGCCATTTTGCGCAAACAGTGAAGGCTCTAAAG
| | | | | ||| || || || | ||| ||| | || | ||| || || || | |||| ||||| || || || || |||| || |||||||||||| | ||||| || |||||||||||||||||||||||||| | || || |||||| | |||
tatgcgtgttttagacaagatgcatatgatctacaaattttttggtatgtttattatacttgcttggaaaattataagaattttgattttcattttgtagTGTGGATTACATTGTTCTAACAAGTGTTGATCGTGATGATCTGCCTGATGGTGGAAGTGGCCATTTTGCTCGGACTGTTAAGGCTATGAAG
upper sequence: LOC_Os05g43576.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S12_246V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacgatccac--cgacgattattgcatt--att-----ggcatgttgagatgataatgcaaaagactttagaaccgatgcttctttttttttttttgcagCGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGGTGGAAGTGGCCATTTTGCGCAAACAGTGAAGGCTCTAAAG
|| | | || | || ||| | |||| ||| || | | | ||| | | ||| | | | | | || || |||||||||| |||||||| |||| || ||||| ||||||||| | ||||||||||| |||| || ||||| | ||||||||| | || |||
-tagggttcatagtgtcgcttaatacattcaatttttgtggaaaatctgaaccatagtcgcagtgacgtaaatcatgtcatgcttgtggattattgtgcagCGTAGGGTATGTTGTATTGACTAGCGTTGACAGAGATGACATGCCTGATGGTGGGAGTGATCACTTTGCTCGAACAGTGAAAACCCTCAAGMapped 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|58682103|gb|CK070790.1|CK070790EST: CCCGATGCCCTGGAGCCTCTCAGGACAGCAGTGGCAGTTGCAAGTTGGGG CGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGG
genomic: CCCGATGCCCTGGAGCCTCTCAGGACAGCAGTGGCAGTTGCAAGTTGGGGgtacgatcca ... ttttttgcagCGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagatgataatgcaaaagactttagaaccgatgcttctttttttttttttgcagCGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGGTGGAAGTGGCCATTTTGCGCAAACAGTGAAGGCTCTAAAG
ccgatgcttctttttt CT-rich tract
ttcttttttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgatccaccgacgattattgcattattggcatgttgagatgataatgcaaaagactttagaaccgatgcttctttttttttttttgcagCGTAGACTATGTTGTGCTGACAAGTGTTGATAGAGATGACCTTCCTGATGGTGGAAGTGGCCATTTTGCGCAAACAGTGAAGGCTCTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG