Sequence
atgc intronic sequence ATGC exonic sequencegtacacacataacactatctgttcataccaacacacacctcatgtatgaagaactaatcttgtattcacatgatttcagGGTTACGATACATTAGTTGGACAGCGTGGCGCTCAGCTTTCAGGGGGGCAGAAGCAAAGGATAGCAATTGCCAGAGCCATACTTAAAAACCCCAAAATCC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g47500.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G843537_T01 (Zea mays), 3'ss of exon 6
gtacacacat-aacactatctgttca-taccaacacacacctcatgtatgaag------aactaatcttgtattcacatgatttcagGGTTACGATACATTAGTTGGACAGCGTGGCGCTCAGCTTTCAGGGGGGCAGAAGCAAAGGATAGCAATTGCCAGAGCCATACTTAAAAACCCCAAAATCC
|||| |||| |||| ||| || || || ||| ||||||| || ||| ||| |||||| | ||||||||||||||| |||||| ||||||||| || || ||||||||||| ||||| |||||||| ||||| || || || || ||||| |||||| |||||||||| |
gtacttacatgaacatgatccacacaataataagccacgg-tcatgtacaaaactataagactgatcatgtatttatatgatttcagGGTTATGATACAACAGTTGGACAACGGGGTGCTCAGCTTTCTGGGGGACAGAAGCAGAGGATTGCGATCGCGAGGGCCATCCTTAAAGACCCCAAAATTC
upper sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------------------------gtacacacataacactatctgttcataccaaca--cacacctcatgtatgaagaacta----atcttgtattcacatgattt-----cagGGTTACGATACATTAGTTGGACAGCGTGGCGCTCAGCTTTCAGGGGGGCAGAAGCAAAGGATAGCAATTGCCAGAGCCATACTTAAAAACCCCAAAATCC
|||| | | | | | | | |||| | | ||| ||| || || | | || || | | ||||| || ||| | || || | | ||| ||||||| || ||||| ||||||||||| || |||||||| |||||||| | || ||||| |||||
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
upper sequence: LOC_Os05g47500.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------------------------------------gtacacacataacactatctgttcataccaacacacacctcat------------gtatgaagaactaatcttgtattcacatgattt-----cagGGTTACGATACATTAGTTGGACAGCGTGGCGCTCAGCTTTCAGGGGGGCAGAAGCAAAGGATAGCAATTGCCAGAGCCATACTTAAAAACCCCAAAATCC
| | || | | | | | || | | || | | | || | || | || | || | || | |||||| ||||| || ||| | || || ||| ||| ||||||| || ||||| ||||||||||| || |||||||| |||||||| | || ||||| | |||||
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataccaacacacacctcatgtatgaagaactaatcttgtattcacatgatttcagGGTTACGATACATTAGTTGGACAGCGTGGCGCTCAGCTTTCAGGGGGGCAGAAGCAAAGGATAGCAATTGCCAGAGCCATACTTAAAAACCCCAAAATCC
aactaat putative branch site (score: 2)
aactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacacataacactatctgttcataccaacacacacctcatgtatgaagaactaatcttgtattcacatgatttcagGGTTACGATACATTAGTTGGACAGCGTGGCGCTCAGCTTTCAGGGGGGCAGAAGCAAAGGATAGCAATTGCCAGAGCCATACTTAAAAACCCCAAAATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG