Sequence
atgc intronic sequence ATGC exonic sequencegtgaggttcctctctgacaatattttctgaattatttgaaatggtggcaaaagTTTATCTGGAACCATTATTTTTAATCCACTTCCATTTTGTGTGAGCATCAGGCTTCATGGTGTTTGTGAGGAAAATCCCCTGGCACCAATTATTGGAAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g53195.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G396856_T02 (Zea mays), 3'ss of exon 4
gtgaggttcctctctgacaatattttctgaattatttgaaatggtggcaaaagTTTATCTGGAACCATTATTTTTAAT-CCACTTCCATTTTGTGTGAGCATCAGGCTTCATGGTGTTTGTGAGGAAAATCCCCTGGCACCAATTATTGGAAGG---------------------------------------------------
||||| | | | | || |||| | || ||| |||||||| |||| ||| | | || | | || ||| | | | | ||||||||||| |||||||| ||||||||| |||||||||| |||||||||
gtgagttccat-----------tcttttgaact-ttcaccatgtgcccaaaagttcatcttgaaggaatgcattgagtgtttttttcatcatttctattgagaagGCTTCATGGCGTTTGTGAAGAAAATCCCTTGGCACCAATAATTGGAAGGCTTGGACTTCCACTGTACCGCACAAGTGGAGACGATTCTGTGCTGTTTGAT
upper sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G000052_T01 (Zea mays), 3'ss of exon 4
gtgaggttcctctctgacaatattttctgaattatttgaaatggtggcaaaagTTTATCTGGAACCATTATTTTTAAT-CCACTTCCATTTTGTGTGAGCATCAGGCTTCATGGTGTTTGTGAGGAAAATCCCCTGGCACCAATTATTGGAAGG---------------------------------------------------
||| | | | || ||| ||||||||||||| || | | | | || || ||| | | | ||||||||||||||| || ||||| ||||||||| |||||||||| |||||||||
------------gtgagttccattctttttagctttcaccatgtgcccaaaagtttatcttgagggaatgtcatgaacatttttttcatcatttttattcatcagGCTTCATGGGGTCTGTGAAGAAAATCCCTTGGCACCAATAATTGGAAGGCTTGGACTTCCACTGTACCGCACAAGTGGTGATGATTCTGTGCTGTTTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaggttcctctctgacaatattttctgaattatttgaaatggtggcaaaagTTTATCTGGAACCATTATTTTTAATCCACTTCCATTTTGTGTGAGCATCAGGCTTCATGGTGTTTGTGAGGAAAATCCCCTGGCACCAATTATTGGAAGG
ctctgac putative branch site (score: 3)
aatattttctgaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggttcctctctgacaatattttctgaattatttgaaatggtggcaaaagTTTATCTGGAACCATTATTTTTAATCCACTTCCATTTTGTGTGAGCATCAGGCTTCATGGTGTTTGTGAGGAAAATCCCCTGGCACCAATTATTGGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG