Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatcttattggctaagtttttgtgtaatataccatagacagcctttggttctgttgtgatgtattaattaatgcagATGTCACCAGAAGATTTCATTAGAAACAATCGAGGTATTGACGATGGGAAAGACCTGCCTGAAGAATTTATGAGGTCCTTATATGAAAGGATTTGGAAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g14260.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 4
gtatgtatcttattggctaagtttttgtgtaatataccatagacagcctttggttctgttgtgatgtattaattaatgcagATGTCACCAGAAGATTTCATTAGAAACAATCGAGGTATTGACGATGGGAAAGACCTGCCTGAAGAATTTATGAGGTCCTTATATGAAAGGATTTGGAAAA
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gtac-tttcttgtggtgaaggttcttttgcggagttct-------ggtttacacaattatgtaacatgttactcgatgcagATGTCACCAGAAGATTTCATTAGAAACAATCGTGGTATCGATGATGGGAAGGACCTACCTGAAGAATTTATGAGATCATTGTATGAAAGGATTTGGAAAA
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 5
------------------gtatgtatcttattggctaagtttttgtgtaat-ataccatagacagcctttggttctgttgtgatgtattaattaatgcagATGTCACCAGAAGATTTCATTAGAAACAATCGAGGTATTGACGATGGGAAAGACCTGCCTGAAGAATTTATGAGGTCCTTATATGAAAGGATTTGGAAAA
| || | |||| | |||| || | | | | || | || | | || | | ||||||||||| | || |||||||| ||||||||||| || ||||| ||||| ||||| ||||||| |||| ||||| |||| | ||| || || | | ||
aaaaagtacaaacttacagggactaaaaacatatttaagcctacaaataattatgatagaaatgatgacttattttcttattggttgttgagttatgcagATGTCTGCTGATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCTGAGGAATACTTGAGGGCCTTGTTTGAGAGAATATCTAGAA
upper sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------gtatgtatcttattggctaagtttttgtgtaatataccatagacagcctttggttctgttgtgatgtattaattaatgcagATGTCACCAGAAGATTTCATTAGAAACAATCGAGGTATTGACGATGGGAAAGACCTGCCTGAAGAATTTATGAGGTCCTTATATGAAAGGATTTGGAAAA
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gtacatatttgagctgtttcgcttagaagctttctgaaatccctcttgaggaatatcttaatacg-atcttgtttg--aagcttgtgattggtcaaacaaagtaactcattactaaatttttcaattacaactt---gcagATGACAGCTGATGGTTTTATTAGAAACAATCGTGGTATAGATGATGGGAAAGATTTGCCTGAGGAATATCTACGTGCATTATATGAAAGGATATCTAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtaatataccatagacagcctttggttctgttgtgatgtattaattaatgcagATGTCACCAGAAGATTTCATTAGAAACAATCGAGGTATTGACGATGGGAAAGACCTGCCTGAAGAATTTATGAGGTCCTTATATGAAAGGATTTGGAAAA
tgatgtattaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatcttattggctaagtttttgtgtaatataccatagacagcctttggttctgttgtgatgtattaattaatgcagATGTCACCAGAAGATTTCATTAGAAACAATCGAGGTATTGACGATGGGAAAGACCTGCCTGAAGAATTTATGAGGTCCTTATATGAAAGGATTTGGAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA