Sequence
atgc intronic sequence ATGC exonic sequencegtcagtcaaagtttttattattgacttgtactattttcatattttgaaaatgtattaacagttctagccttatatgcaaggcaatcagtttgacacattttctattgctactcctcagACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g55410.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 12
gtcagtcaaagtttttattattgacttgtactattttcatattttgaaaatgtattaacagttctagccttatatgcaaggcaatcagtttgacacattttctattgctactcct-cagACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAG
|| || || | ||| ||||||||| || | || | | ||| | ||| ||| ||||||||| || ||||||| |||| | ||||||| ||||||| ||| | ||| ||||||||||||||||| |||||||| ||||| ||||| |||||||||||||||| |||||||||||| |||||| ||||||||||||| ||||| |||
gttggtaaacatgttt-ttattgactcaacatagatccac-tatataaagtatataaactgttctagccatacatgcaagacaattattttgacaaattttcttttgttgttccaacagACTGCACAAGATAATATTGATCTACAGACCACCATTCTTTCTAGATTTGATCAAATCTTTATTGTCAAAGATATCAGAATGTATGACCAAGATAAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 12
gtcagtcaaagtttttattattgacttgtactattttcatattttgaaaatgtattaacagttctagccttatatgcaaggcaatcagtttgacacattttctattgctactcctcagACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAG
|| || || | || | |||| || | || | ||| ||| ||| |||| ||| ||||||||| || ||||||| |||| | ||||||| ||||||| ||||| || |||||| || |||||||| |||||||||||||| ||||| |||||||||||||||||||||||||| || || ||| ||||||||||||||||||| |||
gttggtaaacatgttactcattgtctca-ataatatccatttttgtaaagtgta--aactgttctagccatacatgcaagacaattaatttgacaaattttcttttgctgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 11
gtcagtcaaagtttttattattgacttgtactattttcatattttgaaaatgtattaacagttctagccttatatgcaaggcaatcagtttgacacattttctattgctactcctcagACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAG
| || || | | | ||| || |||| | | | | || | || | | || || | | | | | ||| | || | ||||||||||| ||||||||||| |||||||||| || |||||||| |||||| |||| || ||||| ||||| ||||||||||| ||||||||||
------------gtctactacc-atataaccctcttttatcttttttcagtttgtaaaaaagcatatcgtcat---taaaagagactaatagctgcctttaatgtt-----tttccagACTGCACAGGATAACATTGACTTGCAGACAACTATTCTTTCTAGGTTTGATTTAATTTTCATTGTGAAAGACGTCAGAATGTACAGTCAAGACAAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 11
gtcagtcaaagtttttattattgacttgtactattttcatattttgaaaatgtattaacagttctagccttatatgcaaggcaatcagtttgacacattttctattgctactcctcagACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAG
| ||| || | | ||| || |||| ||||| || ||| | ||| || ||| | | | | || | ||| |||||||||| ||||||||||| |||||||||| || |||||||| |||||| |||| || || || ||||| ||||||||||| ||||||||||
---------gtctactatcataactctcttttatctt----ttttctgtatgtaacaa-------agcataatagtcattacaagagactgatagctgccttgaatgtttttcc--agACTGCACAGGATAACATTGACTTGCAGACAACTATTCTTTCTAGGTTTGATTTAATTTTCATCGTGAAAGACGTCAGAATGTACAGTCAAGACAAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 11
gtcagtcaaagtttttattattgacttgtactattttcatattttgaaaatgtattaacagttctagc-cttatatgcaaggcaatca---gtttgacacattttctattgct--actcctcagACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAG
|||| | | || | || |||| ||| | | | | ||| | ||||| | | | | | |||| | || | | |||||||| || || || || |||||||||||||| || ||||||||||||||||| ||||| ||||| || || |||| | |||| |||||||||
------------------gtttgaaatctggtactctc---ctttggcaatatcatggttttcccgattcttgtttgcaatattcttaagagatgggtgtgtttttttttctttggatttgcagACTGCTCAGGACAATATCGATCTGCAGACAACAATTCTTTCTAGATTTGATCTTATCTTCATTGTCAAGGACATCAGGAAGTATTCCCAAGACAAG
upper sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 11
gtcagtcaaagtttttattattgacttgtactattttcatattttgaaaatgtattaacagttctagccttatatgcaaggcaatcagtttgacacattttctattgctactcctcagACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAG
||| | | || | || | | || || || | |||| | || | | || ||| ||||| | | || | ||| |||||||| ||||||||||| || |||||||||| || ||||| |||||||| | || || ||||| |||||| |||| ||||| ||| || |||
----gtccatggccccttttcttcctcagatttgttctttacttct----tatattcatgcttatgatttactaagca-ggcaactaataaaac----------tacatacattccagACTGCTCAAGATAACATCGACTTGCAGACAACAATTCTTTCAAGATTTGACTTGATTTTCATTGTGAAAGATATCAGGATGTACAGTCAGGATAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagccttatatgcaaggcaatcagtttgacacattttctattgctactcctcagACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAG
gtttgac putative branch site (score: 4)
ctactcctc putative PPT
attttctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtcaaagtttttattattgacttgtactattttcatattttgaaaatgtattaacagttctagccttatatgcaaggcaatcagtttgacacattttctattgctactcctcagACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG