Sequence
atgc intronic sequence ATGC exonic sequencegtactcatctgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatctgatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 4
gtactcatctgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatct-gatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
|||| || | |||||| | | || || | | | | | ||||||||| | ||| | || |||| |||||||| |||| ||||||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||| ||
gtacccaaagcacttagttcacgcggagagagaactt---ttggcgatcaggatgatgctaatgtatattttgaacttattttcagTGAGGTCGGCAAAATTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTCAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 5
gtactcatc-tgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatct-gatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
|| || |||| ||||| || || || || || | | | | ||||||||| | ||| | | |||| |||||||| |||| ||||| ||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||||||
gtgtccaaagcacttagattcacgtggaaagagaac---tcctggcaatcagaatgatgctaatgtatattttaaacttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 4
-------------gtactcatctgcttatgttcacatgaaat-gaaaatctgtcatagaggttgaattgatgctaacttgtatct-gatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
||| | | ||||| | || | || ||| || || | | | | ||||||||| | ||| | | |||| |||||||| |||| ||||| ||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||||||
ggcaccagtaaaagtagaaaacccattatgagtatataacatagaagataactcctggcaatcagaatgatgctaatgtatattttaaacttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 5
---------------gtac-tcatctgcttatgttcacatgaaatgaaaatctgtcataga-------ggttgaattgatgcta--acttgtatctgatcttaattt--cagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
| | || |||| || || || | | | || || | | | || ||| ||| || | | | || |||| |||| || || |||||| | || || ||||||||||| ||||| || || ||||||| ||| ||||| ||||| ||||| || |||||||| || ||
gtataacaagtttatgagcatcttctgatttcattgttatagatttttcacttgctgtatattgccttgtatagtctgtcgctgttactgaaatttatatatgactttgcagTTAGGTCGGCCAAGTTTATTCCGCGCAAGCAATGGGTTGTGGCTGGAGCGGATGATATGTACATCCGTGTATACAATTACAATACAATGGACAAGGTCAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
-----gtactcatctgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatctgatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
|| | | || || | | | || ||| || | | | |||| || ||| ||| | || | |||| ||||||||||| || ||| ||||||| || |||||||||||||| || || || ||||| ||||||||||||||||||||||| ||||| || | ||
gtatgatatatagcatctcattgttccttcttat-----tctttcgcacatcatttgttgaatct---ctgt-cctggtgttg--tgcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------------gt-actcatctgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatctgatctta--atttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
|| | | | | | | | || | | | || ||| || || ||| || | | || || | | ||| ||| |||| ||||||| || ||||| |||| || ||||||||||| ||||| || || |||||||| |||||||| ||||| || ||||| ||||| || |||||
gtatgtacatgtactttatctgtttccatatgctctatttggtgtgattgaattcccttgatccatttttactcaatttctctcttattggtaaggttattacatgtttcaattttacattatcattgcagTTAGGTCAGCGAAGTTTATAGCACGCAAGCAATGGGTTGTTGCTGGAGCTGATGATATGTTTATTCGTGTATACAATTATAACACAATGGATAAGGTTAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------gtactcatctgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattga----tgctaacttgtatctgatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
|| || | |||| ||| | || | | | ||||| | | || | | || || || |||| || ||||||||||||||| | || || || ||| | ||||| || | ||||| ||||||||||| ||||||||||| ||||||||||| ||||| ||
gttgcatttttactttcttccagctttgtttccatttcaaagttattgatgaaattcactgaatgaagttcttctcattcactccttccgtttcttgcagTTCGATCAGCAAAATTTATTCCTCGCAAGCAGTGGATAGTAGCGGGCTCTGACGACATGTTCATTCGAGTCTACAACTATAACACGATGGATAAAGTGAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ09529 (Selaginella moellendorffii), 3'ss of exon 2
-------------------------------------gtactcatctgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatctgatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
||| | || | ||| | | | | | | || || | | | | |||| | |||| || ||| || || || || || || || || || || ||| | || |||||||| ||||| |||| |||||| |||||||||||||| || |||||||| || ||
gtaacttttggagtggatttctctaagtccctcgagagtatttttccaagtctgtgttgctccatctcgatttttcta---agtttctctctaaacca--ttgtgtgatctcttgcttgtagTCCGCTCGGCCAAGTTCATATCGCGAAAGCAGTGGATAGTCGCTGGTGCCGACGACATGTACATTCGAGTCTACAACTACAATACCATGGACAAGGTCAA
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ36319 (Selaginella moellendorffii), 3'ss of exon 2
---------------------------------gtactcatctgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatctgatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
| || | | || | | | || | | | | | || |||| | |||| || ||| || || || || || || || || || || ||| | || |||||||| ||||| |||| |||||| |||||||||||||| || |||||||| || ||
gtaacttttggagtaaatttctctaagtcccttgagagtatttttccaagtctgtgttgc-tccatctcgatttttctaagtttctctctaaaaaattgtgtgatctcttgcttgtagTCCGCTCGGCCAAGTTCATATCGCGAAAGCAGTGGATAGTCGCTGGTGCCGACGACATGTACATTCGAGTCTACAACTACAATACCATGGACAAGGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatctgtcatagaggttgaattgatgctaacttgtatctgatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
atcttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcatctgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatctgatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA