Sequence
atgc intronic sequence ATGC exonic sequencegtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.4 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 20
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatct-atgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
||| ||| |||||||||| || || ||| || | || ||| | | |||||| | |||| |||||| | ||| || ||||||||||||||||| ||| |||| ||||| |||||||| |||||||| | |||||||| ||||| |||||| | ||||| ||||||
------gtaaatcttgtttgctgtgattaaatccttgttttggtgctcttcctttgagaactaaacattatcttgtgtattctgcagTAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAAAGTACCAGAGATAGTGGCAATTTGGAGAGACGACCTGAGTAAA------
upper sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 19
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatcta-tgtatta-----tacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
||| || |||||||||| || || ||| || | || ||| | |||||||| | |||| |||||| | ||| | ||||||||||||||||| ||||||| || || |||||||| |||||||| | || ||||||||||| |||||||| ||||||||||||
------gtaagtcttgtttgctgtgattaaatccttgttctggtgctgttcctttgagagctaaacattatcttctgtattcggcactgcagTAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA------
upper sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 5
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatct-atgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
||| ||| |||||||||| || || ||| || | || ||| | | |||||| | |||| |||||| | |||||| ||||||||||||||||| ||| |||| ||||| |||||||| |||||||| | |||||| | ||||| |||||| | ||||| ||||||
------gtaaatcttgtttgctgtgattaaatccttgttttggtgctcttcctttgagaactaaacattatcttgtgtattctgcagCAACCGTATACCTGAAGCTGCATTACTGGCGCGTTCATATCTTCCTAGCAAAGTACCAGAGATATTGGCAATTTGGAGAGACGACCTGAGTAAA------
upper sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 20
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattat-acagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
|| | | ||||| || | | | | || | |||| | || | || | ||| | |||| || || ||||| |||||||| | |||||||||||||||||||| ||||||||||| ||||||||||| ||||||| | || ||||| ||
--gtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacagTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG------
upper sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 20
---gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
| ||| | | || ||| ||| | ||| | | | || | || || || ||| | || ||| || || ||||| |||||||| | |||||||| || |||||||| ||||||||||||||||||||||| | ||||| || || ||||| ||
gtaattcattagtagtcacttgagagtttggaaaatcaaattt--atgcacctttggttaa--ctgtgtgacaa-tattttttcctcagTAACCGGATACCAGAAGCTGCTCTGATGGCACGATCATATCTTCCGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG------
upper sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 20
---------------------------------------------------------------------------gtacatgtacatcctgtttgctgtt-atgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
| | ||| || | | ||| || || || | | | | ||| | | | || || | || | | ||| ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| ||| | |||||| | | || |||||||||||||||| ||
gtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatg-gtctgttgcagTAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAG------
upper sequence: LOC_Os06g05180.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 20
gtacatgtacatcctgtttgctgttatgaactcc----ccattgtagtaa-atcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
||| ||| | | ||| ||| | |||| | | || || | | | || | || | | ||||||||| || ||||| ||||| || |||||||| ||||||||||| ||||| || || |||||||| || | ||||| || ||||| | |||
gtaattgt-tgttgttactgcaaacatgggaacaaagatagttgtggagatattccacttttgggatgatactgaagcattctctttgcagCAATCGGATCCCTGAGGCTGCTTTGATGGCACGGTCTTATCTTCCAAGCAAGGTCTCAGAGATAGTCGCTCTGTGGAGGAAAGACCTTAATAAG------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
agctaaa putative branch site (score: 3)
taaatcatttttcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatgtacatcctgtttgctgttatgaactccccattgtagtaaatcatttttcaaagctaaacctcatctatgtattatacagCAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAGTAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA