Sequence
atgc intronic sequence ATGC exonic sequence...tggagctgattagatccctcggtactgagattcatttctgttacttccattttctgcacaagatgtttcatatttatcatcagctatctgtgggatgcagGTGGCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62040.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G018697_T02 (Zea mays), 3'ss of exon 4
--tggagctgattagatccctcggtactgagattcatttctgttacttccattttctgcacaagatgtttcatatttatcatcagctatctgtgggatgcagGTGGCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
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cattgagaaaatgcactatatttgcattttgggttactgtatctatttt-gctatcttcatttgttgctttacgttactcattatctgcatatgg-atatagGTGGCAGTGGGTGATGTTATATACATCGAAGCAAATAGTGGAGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 4
tggagctgattagatccctcggtactgagattcatt-tctgtt----acttccattttctgcacaagatgtttcatatttatcatcagctatctgtgggatgcagGTGGCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
||||| ||| ||| | | |||| | | || ||| || | ||| || |||||| | || || | || |||| || || ||| || |||||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||
----gctgagtagctccttaaacattgagttaccttatctattctgtatttctgttatctgcatttgttgctttaggttactcattgtctgcctatgg-atatagGTGGCAGTGGGTGATGTTATATACATTGAAGCAAATAGTGGAGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATATGATCTTGAAGCTG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 4
---tggagctgattagatccctcg-gtactgagattcatttctgttacttccattttctgcacaagatgtttcatatttatcatcagctatctgtgggatgcagGTGGCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
|| | || | || | | || ||||| | | | || ||| ||||| | ||| | | || || || | | ||||||| || || |||||||||||||| ||||||| |||||||| || || ||||| || || ||| ||||| ||||||||||||||| || ||||| || |
atcattagtttataggtctacttgcatgcttagattgttatttttttcttttattttttatttt--gtgtatggt-ttcattatttttcaa-tacaatctgcagGTAGCTGTTGGTGATGTTATATATGTTGAAGCCAATAGTGGAGCTGTTAAAAGGGTGGGCAGAAGTGATGCTTTTGCTACAGAATTTGACCTTGAGGCGG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 4
tggagctgattagatccctcggtactgagattcatttctgttacttccattttctgcacaagatgtttcatatttatcatcagctatctgtgggatgcagGTGGCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
| |||| | | | | || | || | | | |||| ||||| |||||||| ||||| || ||||||||||| || || ||||| |||||| ||||||| || ||||| |||| || || |||| ||| |||||||| |
-------------------------------------------gtgatggtttccg---acggttttgctctttgctggttttgaaactgttatcgtcagGTAGCAGTGGGAGATGTCATCTACATTGAAGCCAACAGCGGTGCTGTGAAACGAGTTGGACGAAGTGATGCTTTCGCGACCGAATTCGACCTTGAAGCGG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 4
tggagctgattagatccctcggtactgagattcatttctgttacttccattttctgcacaagatgtttcatatttatcatcagctatctgtgggatgcagGTGGCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
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---------------------------------------------gtgatggtttcca-acggttttgctctttgctggttttgaaactgttatcgtcagGTAGCAGTGGGAGATGTCATCTACATTGAAGCCAACAGCGGTGCTGTGAAACGAGTTGGACGAAGTGATGCTTTCGCGACTGAATTCGACCTTGAAGCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccattttctgcacaagatgtttcatatttatcatcagctatctgtgggatgcagGTGGCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
atgtttcatatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggagctgattagatccctcggtactgagattcatttctgttacttccattttctgcacaagatgtttcatatttatcatcagctatctgtgggatgcagGTGGCAGTGGGTGATGTTATATACATTGAAGCTAATAGTGGTGCAGTGAAAAGAGTTGGTAGATGTGATTCTTTTGCTACAGAATACGATCTTGAAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - gctgatt
- - - - - - - - - - ggtactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcagc