Sequence
atgc intronic sequence ATGC exonic sequence...attgttttgctcccggttctttcccaacttatgtataccatcttaatattttttttgttacattctgtttcatttctctctcttttttctggccttgcagGTATTTTCTACCTATACATGAAAACAGCTGAAAGAGCCCATCTTCCGAACAAATTATGGGAGAGGGTCAAACTACCCAGAAATTATGAGAAAGCAATGGA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g16950.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g16950.5 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G461793_T01 (Zea mays), 3'ss of exon 2
attgttttgctcccggttctt--tcccaacttatgtataccatcttaatattttttttgttacattctgtttcatttctctctcttttttctggccttgcagGTATTTTCTACCTATACATGAAAACAGCTGAAAGAGCCCATCTTCCGAACAAATTATGGGAGAGGGTCAAACTACCCAGAAATTATGAGAAAGCAATGGA
|| || |||| | || | | | || | || | | ||||| | | ||| ||| | ||| | || ||||||||||||||| || || |||||||| || |||||||| ||||| || ||||||||||||||||| |||||||| || | ||||||||||||||||||||
ttttttgtgctatgaactattaaccttgaagggagcctatgcttacaaaaatctttttctgatgctct--catgtttttttcttcctcaatcggttatgcagGTATTTTCTATCTGTATATGAAAACCGCCGAAAGAGCTCATCTGCCAAACAAATTATGGGAGAGAGTCAAACTGCCGAAGAATTATGAGAAAGCAATGGA
upper sequence: LOC_Os07g16950.5 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0030g01480.t01 (Vitis vinifera), 3'ss of exon 12
----attgttttgctcccggttctttcccaacttatgtataccatcttaatattttttttgttacattctgtttcatttctctctcttttttctggccttgcagGTATTTTCTACCTATACATGAAAACAGCTGAAAGAGCCCATCTTCCGAACAAATTATGGGAGAGGGTCAAACTACCCAGAAATTATGAGAAAGCAATGGA
||| | | ||||| || || || | | || | | | || | | |||| | ||||| || || |||||| | || || |||||||||||||| ||||||||||||| | || |||||||||||||| |||| ||| | || |||| || | || || | ||
tgtgatttatggattgtttcctctttattaaatttagttctttagatcaaagctgtatgtggctgactatgttaatgattggtctctggttcttg----tgcagGAGTGTTTTATCTATACATGAAAACCATTGAAAGAGCCCATATGCCAAACAAATTATGGGAACGGGTTAAATTGCCACGAAACTACGGAAAGGCTCTTGA
upper sequence: LOC_Os07g16950.5 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv17s0000g09220.t01 (Vitis vinifera), 3'ss of exon 3
----attgttttgctcccggttctttcccaacttatgtataccatcttaatattttttttgttacattctgtttcatttctctctcttttttctggccttgcagGTATTTTCTACCTATACATGAAAACAGCTGAAAGAGCCCATCTTCCGAACAAATTATGGGAGAGGGTCAAACTACCCAGAAATTATGAGAAAGCAATGGA
||| | | ||||| || | | | | || | | | || | | |||| | ||||| || || |||||| | || || |||||||||||||| ||||||||||||| | || |||||||||||||| |||| ||| | || |||| || | || || | ||
tgtgatttatggattgtttcctctttattaaaattacttctttagatcaaagctgtatgtggctgactatgttagtgattggtctctggttcttg----tgcagGAGTGTTTTATCTATACATGAAAACCATTGAAAGAGCCCATATGCCAAACAAATTATGGGAACGGGTTAAATTGCCACGAAACTACGGAAAGGCTCTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattttttttgttacattctgtttcatttctctctcttttttctggccttgcagGTATTTTCTACCTATACATGAAAACAGCTGAAAGAGCCCATCTTCCGAACAAATTATGGGAGAGGGTCAAACTACCCAGAAATTATGAGAAAGCAATGGA
tcttaat putative branch site (score: 3)
cattctgtttcatttc putative PPT
ttttttgttacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgttttgctcccggttctttcccaacttatgtataccatcttaatattttttttgttacattctgtttcatttctctctcttttttctggccttgcagGTATTTTCTACCTATACATGAAAACAGCTGAAAGAGCCCATCTTCCGAACAAATTATGGGAGAGGGTCAAACTACCCAGAAATTATGAGAAAGCAATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA