Sequence
atgc intronic sequence ATGC exonic sequencegtaagcgcttccagcgatctgattcgattcctcttcttgggggactcggggttttgatcctgcaaacctttgcagTACGAGGAGGAGAAGATTGGAGAGGGCACGTACGGGGTAGTGTACAAGGCGCGGGACAAGGTCACCAACGAGACGATCGCGCTCAAGAAGATCCGGCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01850.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 1
---------------------gtaagcgcttccagcgatctgattcgattcctcttcttggggg-actcggggttttgat--cctgcaaacctttgcagTACGAGGAGG---AGAAGATTGGAGAGGGCACGTACGGGGTAGTGTACAAGGCGCGGGACAAGGTCACCAACGAGACGATCGCGCTCAAGAAGATCCGGCTTG
| | ||| | | ||||||| | || ||| | | |||| | | | ||| | ||||||||||| ||| ||||||| || ||||||||||||||||| ||||||||||||| |||||||| ||||||||||||||||||||||||||||||||| |
gtaagcgagcgatctggcccgattcgggctcgaggttttttgattcggtctgtccgattgagcgtgctcgtctgtccgcctgcgtgcgtgctgctgcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC---
upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 1
--------------------gtaagcgcttccagcgatctgattcgattcctcttcttggggg------actcg----gggttttgatcctgcaa--acctttgcagTACGAGGAGG---AGAAGATTGGAGAGGGCACGTACGGGGTAGTGTACAAGGCGCGGGACAAGGTCACCAACGAGACGATCGCGCTCAAGAAGATCCGGCTTG
| | || || | | ||||| | || |||| | | | | |||| | | | | |||| | | ||||||||| ||| ||||||| || ||||||||||||||||| ||||||||||||| |||||||| ||||||||||||||||||||||||||||||||| |
gtaagcgagcgatctggcccgattcggactcgagggttttgatttggtttctctgatcgagtgtgttctgctcgtcgcgtgcgtgcgtgctgctgctgctgcttcagTACGAGAAGGTGGAGAAGATCGGGGAGGGCACGTACGGGGTGGTGTACAAGGCGCTGGACAAGGCCACCAACGAGACGATCGCGCTCAAGAAGATCCGCC---
upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S25_198V6.5 (Physcomitrella patens), 3'ss of exon 2
------------------gtaagcgcttccagcgatctgattcgattcctcttcttgggggactcggggttttgatcc-tgcaaaccttt------gcagTACGAGGA---GGAGAAGATTGGAGAGGGCACGTACGGGGTAGTGTACAAGGCGCGGGACAAGGTCACCAACGAGACGATCGCGCTCAAGAAGATCCGGCTTG
|| | | | ||| | || | | | | ||| ||| || | || ||||| ||| | ||||||||||||||||||||| ||||| || || |||||||| ||||| |||| || || || || || || || || || ||||
tatgactaatcgagaggtttactctttcttacaaggctgtagaaactcttaagtacatgttattaatagttccattccatgatggctgttctaatgacagTATGAGAAAGTGGAGAAGATTGGAGAGGGCACATACGGTGTCGTATACAAGGCCCGGGATCGCCTCACTAATGAAACTATTGCTCTGAAAAAAATACGGC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattcgattcctcttcttgggggactcggggttttgatcctgcaaacctttgcagTACGAGGAGGAGAAGATTGGAGAGGGCACGTACGGGGTAGTGTACAAGGCGCGGGACAAGGTCACCAACGAGACGATCGCGCTCAAGAAGATCCGGCTTG
ttttgat putative branch site (score: 4)
cctttgc putative PPT
ttttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcgcttccagcgatctgattcgattcctcttcttgggggactcggggttttgatcctgcaaacctttgcagTACGAGGAGGAGAAGATTGGAGAGGGCACGTACGGGGTAGTGTACAAGGCGCGGGACAAGGTCACCAACGAGACGATCGCGCTCAAGAAGATCCGGCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG