Sequence
atgc intronic sequence ATGC exonic sequencegtacactgttatataatatgacctcaagtcctcaaccttttcccgtttgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g55150.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G178996_T01 (Zea mays), 3'ss of exon 2
gtacactgttatataatatgacctcaagtcctcaaccttttcccgtt--tgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
||| |||| | || || | | || ||| | || || | | | |||| || | |||| | || |||||| ||| |||||||||| |||||| || ||||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||||||||
gtatgctgt-aaatcatttaatct--agtaat-aatctccacacatcactgacatgta-acgaatgcacatgtacaatgttggatggccagGTTAGGAGCTCTGTGAAACTTAAGCGAGTGATGCAGACAATTCTTTCTTTGGGAAACGCATTAAACCAAGGAACTGCAAGGG
upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G36440.1 (Glycine max), 3'ss of exon 15
-----------------------gtacactgttatataatatgacctcaagtcctcaaccttttcccgtttgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
||| || | || ||| | ||| ||||| | | | || ||| ||| || | | || | | ||| | ||||| ||||| || | ||| || | ||||||||||| ||||| || |||||||| || |||||||||||||| | ||
gcatgatatcttcctttttacggaaacatctttttgcaacatggttcctttctctct-ttttttcatgagaaataacattttggatgttgtgattttgttttctcttttcagATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTAGGAAATGCTTTGAACCAAGGAACTGCCAAGG
upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G08230.1 (Glycine max), 3'ss of exon 13
-----------------------gtacactgttatataatatgacctcaagtcctcaaccttttcccgtttgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
||| || | || || || || ||||| | | | || ||| || || | | | | | ||| | ||||| ||||| || | ||| || | ||||||||||| ||||| || |||||||| || |||||||||||||| | ||
gcatgatatcttcctttttacggaaacatctttttgcaacatagtttc----tttctcttttttcatgagaaataacattttggatgttgagattttgtttcctctattcagATCAGGAATTCTGTCAAATTAAAGAGAATTATGCAAACAATACTTTCTTTAGGAAATGCTTTGAACCAAGGAACTGCCAAGG
upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ15040 (Selaginella moellendorffii), 3'ss of exon 10
gtacactgttatataatatgacctcaagtcctcaaccttttcccgtttgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
|||| | | || ||| || | | ||| ||||| | | ||| ||||||||| ||||||||||||| |||| || |||||||||| ||||||||||||||||| || |
----------------------------------gtaatttcgcactc------ttcttgtatgttgcc-tgaagccggattcttgcagGTGAAAGAGTCTCCTAAGCTTAAAAGAGTGATGCAAACGGTTCTGTCCCTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG
upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ14916 (Selaginella moellendorffii), 3'ss of exon 6
gtacactgttatataatatgacctcaagtcctcaaccttttcccgtttgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
| ||| | ||| ||||||| | ||||||||||||| |||| || ||||||||| ||||||||||||||||| || |
-------------------------------------------------------------------------------------gtaagttgcagagtctcctaagCTTGAAAGAGTGATGCAAACGGTTCTGTCCCTGGGAAATGTGTTAAACCAAGGAACTGCTAGAG
upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ36895 (Selaginella moellendorffii), 3'ss of exon 10
gtacactgttatataatatgacctcaagtcctcaaccttttcccgtttgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
|| || | |||| | ||| | ||| | |||| ||||| | | |||| |||||||| |||| |||||||| |||| || ||||||||||| |||||||||||||||| || |
-------------------------------gtaatctcccactgtttt-----tgtaagtagcctga-----agccggatttttgcagGTGAAAGAGTCTGCGAAGCTTAAAAGAGTAATGCAAACGGTTCTATCCTTGGGAAATGCGCTAAACCAAGGAACTGCTAGAG
upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ33545 (Selaginella moellendorffii), 3'ss of exon 10
gtacactgttatataatatgacctcaagtcctcaaccttttcccgtttgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
|| || | |||| | ||| | ||| | |||| ||||| | | |||| ||||||||| |||| |||||||| |||| || ||||||||||| |||||||||||||||| || |
-------------------------------gtaatctcccactgtttt-----tgtaagtagcctga-----agccggatttttgcagGTGAAAGAGTCTGCTAAGCTTAAAAGAGTAATGCAAACGGTTCTATCCTTGGGAAATGCGCTAAACCAAGGAACTGCTAGAG
upper sequence: LOC_Os02g55150.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ38303 (Selaginella moellendorffii), 3'ss of exon 3
--------------------------gtacactgttatataatatgacctcaagtcctcaaccttttcccgtttgacga-gtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
|| || ||| | | | | | || || | | | || | || |||| | || || | | | | | | ||| | ||| ||||||| | ||||||||||||| |||| || |||||||||| ||||||||||||||||| || |
gtcaaaattattttgtctaccctttcaaacgttggtatcaggtgtcagatttacgagaaaatctggtagtagtcaatgaagcttcaaca-gaggtaatttcgactcttcttg-taagttgcagAGTCTCCTAAGCTTGAAAGAGTGATGCAAACGGTTCTGTCCCTGGGAAATGCGTTAAACCAAGGAACTGCTAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accttttcccgtttgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
gtttgac putative branch site (score: 4)
tgttatataatgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacactgttatataatatgacctcaagtcctcaaccttttcccgtttgacgagtttaaacatgctgttatataatgttatttggacagGTTAGGAACTCTGTTAAGCTTAAGCGAGTGATGCAAACAATTCTTTCGTTGGGAAATGCATTAAACCAAGGAACTGCAAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA