Sequence
atgc intronic sequence ATGC exonic sequence...tatgctaatttatttcttaatgtgcatgccattatttttaatcgagtatcattactgtggattctacgtcttaaagatggactatctaatctgcatttagGTGGCACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g13570.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 3
------tatgctaatttatttcttaatgtgcatgccattatttttaat-cgagtatcattactgtggattctacgtcttaaagatggactatctaatctgcatttagGTGGCACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
|| | | | | | | | | ||| | ||||| || | | | | | ||||| | |||| ||| ||||| || || ||||| ||| ||||||||||| ||||||||||| | ||||||||||||||||||||| ||||||||||| ||||| || || ||||||||| | ||||||||||||||||||
aggcatcata-tggtatgtctttgcaaattcattcaattatgggtactataaatgtgttaactgtagtttct-----ctaaccatggattagcttatctg-attcagGTGGCACAATCATCTTAACCCAGCCATAAACAAGGAGGCATGGACGCAAGAAGAGGAGATTACTCTTATTCATGCTCATAGGATGTATGGAAATAAATGG
upper sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G32730.1 (Arabidopsis thaliana), 3'ss of exon 6
tatgctaatttatttcttaatgtgcatgccattatttttaatcgagtatcattactgtggattctacgtct-taaagatggactatctaatctgc-atttagGTGGCACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
| | ||| || | | | || | ||| | | ||| ||| | ||| || | || || || | | | || ||||||||| ||||||||||||||||| || || || | |||||||| || ||||||||| | || || || | ||| |||| ||| ||||| |||||||||
-gtaatgcaaaggctctcaacttctttccgataa-----aatgatatttacatacattgggtggtacttcaacgcacataaacaatattgtgggtgatgtagGTGGCATAACCATCTTAACCCTGGGATTAATAAAAATGCATGGACTCAGGAAGAGGAACTGACTCTTATTCGTGCGCATCAAATTTATGGGAATAAATGG
upper sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G11510.1 (Arabidopsis thaliana), 3'ss of exon 6
-tatgctaatttatttcttaatgtgcatgccattatttttaatcgagtatcat-tactgtggattctacgtcttaaagatggactatctaatctgc-----atttagGTGGCACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
|||||| || | || | | || | | || | || | || || | | | || | | | | ||| | | ||| || |||||||||||| ||||| || |||| ||||||||| || || ||||| |||||||| || | || || | |||||||| ||| ||||| |||| ||||
gtatgcttatagagacagctatttctctaacaacagtgttttactagcactatatagtttttgtcctcttttcaagattttaactgtgaaggctgttactgatatagGTGGCACAATCATCTCAATCCTGCCATAAACAAAGAAGCTTGGACTCAAGAAGAAGAGCTGCTTCTGATTCGTGCTCATCAAATATATGGTAATAGATGG
upper sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 5
tatgctaatttatttcttaatg-tgcatgccattatttttaatcgagtatcattactgtggattctacgtcttaaa-gatggactatcta-atctgcatttagGTGGCACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
||||| | ||| || ||| | ||| ||| ||| | | | | | || | | | || | | || | || || |||||||||||||| || ||||| |||| ||||||||||||||||||||| |||||||| || | | | | | |||||||| || |||||||| || |||
--tgctattatatacattcatgatacatttgattgctttaggtttt-tctgccttccgttattaaaagctattgtatgctgtgttgcctgtattaatttttagGTGGCACAATCACCTTAATCCTGCCATAAACAAGGAGGCATGGACTCAAGAAGAAGAGTTGGCATTGGTTCGTGCTCATCAGATATATGGAAACAAGTGG
upper sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 5
tatgctaatttatttcttaatgtgcatgccattatttttaatcgagtatcattactgtggatt--ctacgtcttaaagatggactatctaatc--tgcatttagGTGGCACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
| ||||| | |||| | | |||| ||| | || | || |||| | || | || | | ||| | | || ||||||||||| ||||| || |||| |||||||||||| |||||||| |||||||||||| | | | || |||||||||| ||| ||||| || || |||
--tctatgattattctatgatgt--ttcttttggcttttgatcactttgttaggatgagaatgtgctactttttctacttgcatggattgatccttcctttcagGTGGCACAATCATCTAAATCCTGCCATAAACAAGGAAGCATGGACTCAAGAAGAGGAACTGGCTTTAATTCATGCTCATCAAATTTATGGGAACAAGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatcattactgtggattctacgtcttaaagatggactatctaatctgcatttagGTGGCACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
atctaat putative branch site (score: 3)
ttaaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgctaatttatttcttaatgtgcatgccattatttttaatcgagtatcattactgtggattctacgtcttaaagatggactatctaatctgcatttagGTGGCACAACCATCTTAACCCTGGCATAAACAAGGAGGCATGGACACAAGAAGAGGAAATTACCCTCATACATGCTCATCGAATGTATGGAAATAAATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- tgctaat
- - - - - - - - - - - tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggac