Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtagttcttttccttcattacttaacctggaattatttaaaacattggctttttagtttttattcaagttatgtaatgtagatcacattatttggggaagttaaactgatattctttcatgcattgtttccagCTTCAATGTTTGAAGAAATGCCCTGGTAACTATCTGCAAGCATTAAAGAGTATACCAAGAACATTACGAATGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g43374.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G307981_T01 (Zea mays), 3'ss of exon 6
gtaagtgtagttcttttccttcattacttaacctggaattatttaaaacattggctttttagtttttattcaagttatgtaatgtagatcacattatttggggaagttaaactgatattctttcatgcat-tgtttccagCTTCAATGTTTGAAGAAATGCCCTGGTAACTATCTGCAAGCATTAAAGAGTATACCAAGAACATTACGAATGAT----------------------
|| | | | ||| || || || | || | | | || ||| || | || || | ||| | | |||||||||||||||||| |||||||||||||||||||| |||| |||||| | ||| |||||||||||||| | |||||||
----------------------------------------atgtggccttataattctttgtgccttgtttaaagcacatagttttgtacattttaactgattatttttttcttttcttccgttgtttgcatgtttccagCTTCAATGTCTGAAGAAATGCCCTGGTAACCATCTACAAGCACTCAAGGGTATACCAAGAACACTGAGAATGATGTATGTTGCATTTTTTATTTAA
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G096553_T02 (Zea mays), 3'ss of exon 10
gtaagtgtagttcttttccttcattacttaacctggaattatttaaaacattggctttttagtttttattcaagttatgtaatgtagatcacattatttggggaagttaaactgatattctttcatgcat-tgtttccagCTTCAATGTTTGAAGAAATGCCCTGGTAACTATCTGCAAGCATTAAAGAGTATACCAAGAACATTACGAATGAT
|| | | | ||| || || || | || | | | || ||| || | || || | ||| | | |||||||||||||||||| |||||||||||||||||||| |||| |||||| | ||| |||||||||||||| | |||||||
----------------------------------------atgtggccttataattctttgtgcgttgtttaaagcacatagttttgtacattttaactgattatttttttcttttcttccgttgtttgcatgtttccagCTTCAATGTCTGAAGAAATGCCCTGGTAACCATCTACAAGCACTCAAGGGTATACCAAGAACACTGAGAATGAT
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G427822_T01 (Zea mays), 3'ss of exon 9
gtaagtgtagttcttttccttcattacttaacctggaattatttaaaacattggctttttagtttttattcaagttatgtaatgtagatcacattatttggggaagttaaactgatattctttcatgcat-tgtttccagCTTCAATGTTTGAAGAAATGCCCTGGTAACTATCTGCAAGCATTAAAGAGTATACCAAGAACATTACGAATGAT
|| | | | ||| || || || | || | | | || ||| || | || || | ||| | | |||||||||||||||||| |||||||||||||||||||| |||| |||||| | ||| |||||||||||||| | |||||||
----------------------------------------atgtggccttataattctttgtgccttgtttaaagcacatagttttgtacattttaactgattatttttttcttttcttccgttgtttgcatgtttccagCTTCAATGTCTGAAGAAATGCCCTGGTAACCATCTACAAGCACTCAAGGGTATACCAAGAACACTGAGAATGAT
upper sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G04820.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaagtgtagttcttttccttcattacttaacctggaattatttaaaacattggctttttagtttttattcaagttatgtaatgtagatcacattatttggggaagttaaac--tgatattctttcatgcattgtttc----cagCTTCAATGTTTGAAGAAATGCCCTGGTAACTATCTGCAAGCATTAAAGAGTATACCAAGAACATTACGAATGAT
|| ||||| | | | ||||| | | | | | ||| || || | |||| ||| || |||| ||||| || ||| |||||||||||||||||||||| ||||| || | || | || || ||||| || |||||||
----------------------------------------------------------gtaagttttaaactactcatgta---ttggtttctacaattgatgagtttccatgatgatcagttttaatcgggcgttttgaaacagCTGCAGTGTCTGAAGAAATGCCCTGGTAACTACCTGCAGGCTCTTAAAGGCATTCCCAGAACTTTGAGAATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagatcacattatttggggaagttaaactgatattctttcatgcattgtttccagCTTCAATGTTTGAAGAAATGCCCTGGTAACTATCTGCAAGCATTAAAGAGTATACCAAGAACATTACGAATGAT
aactgat putative branch site (score: 3)
ttgtttcc putative PPT
acattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtagttcttttccttcattacttaacctggaattatttaaaacattggctttttagtttttattcaagttatgtaatgtagatcacattatttggggaagttaaactgatattctttcatgcattgtttccagCTTCAATGTTTGAAGAAATGCCCTGGTAACTATCTGCAAGCATTAAAGAGTATACCAAGAACATTACGAATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC