Sequence
atgc intronic sequence ATGC exonic sequence...acatgaaaatgtttgtggtactttaatcagctagggagtgattagatgaatatgcagcatcacactattgatgctaatgcttcacgtttcctatctatagGTTTTGTTGGGTATGCCATTCTTGTTATCACATCCAGTTGAGTACATCTCACGAGCATTCAATCTTGGGCGTGTCTTCATCCATTTCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g07720.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g07720.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G066362_T01 (Zea mays), 3'ss of exon 7
----acatgaaaatgtttgtggtactttaatcagctagggagtgattagatgaatatgcagcatcacactattgatgctaatgcttcacgtttcctatctatagGTTTTGTTGGGTATGCCATTCTTGTTATCACATCCAGTTGAGTACATCTCACGAGCATTCAATCTTGGGCGTGTCTTCATCCATTTCTG
|| | ||| | | || | | ||| ||||||| ||| | ||| ||| || | |||||| || || |||| |||| ||||||||||||||||||||||||||| | |||||||||||||||||||||||| ||||||||||||| || || || || |||||||||||
ccctttatccttaaacttgagtgtgtctagtatgtctgggg----ttagatggatacaaggtatcgcacagtttgtactaatgatttacaattcccatctgtagGTTTTGTTGGGTATGCCATTCTTGCTGTCACATCCAGTTGAGTACATCTCAAGAGCATTCAATCTCGGTCGCGTGTTTATCCATTTCTG
upper sequence: LOC_Os01g07720.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G37130.1 (Glycine max), 3'ss of exon 6
acatgaaaatgtttgtggtactttaatcagctagggagtgattaga-tga---atatgcagcatca-cactattgatgctaatgctt-cacgtttc-ctat--ctatagGTTTTGTTGGGTATGCCATTCTTGTTATCACATCCAGTTGAGTACATCTCACGAGCATTCAATCTTGGGCGTGTCTTCATCCATTTCTG
| | | | | ||| || || | | | |||| ||| || | || | | | || | ||| | | | | || ||| ||| || | || |||| | || ||| || | ||| | |||||| ||||| ||| |||| ||||| ||||| ||||||||||||||||||||
--------gtttctcttgggcttcaa-cattgattggttctctagagtgagcaatgtccaattttggtaatgttagttataactcctatatggttaactactgctacagATATTACTGGGACTTCCTTTCCTGGTTTCATACCCAGTTACATACATATCAAGAGCCTTCAACCTTGGCCGTGTCTTCATCCATTTCTG
upper sequence: LOC_Os01g07720.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G39740.1 (Glycine max), 3'ss of exon 6
acatgaaaatgtttgtggtactttaatcagctagggagtgattagatgaatatgcagcatcaca-ctattgatgctaatgcttcacgtttcctatctatagGTTTTGTTGGGTATGCCATTCTTGTTATCACATCCAGTTGAGTACATCTCACGAGCATTCAATCTTGGGCGTGTCTTCATCCATTTCTG
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atattgtcaggtgagtttctcttcttgggcatcaagattgattggttctctagagtgagcaatgtccaattttggtaaca-ttagtgaactcttgctacagATATTATTGGGGCTTCCTTTCCTGGTTTCATATCCAGTTGCATACATATCAAGAGCCTTCAATCTTGGCCGTGTCTTCATCCATTTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaatatgcagcatcacactattgatgctaatgcttcacgtttcctatctatagGTTTTGTTGGGTATGCCATTCTTGTTATCACATCCAGTTGAGTACATCTCACGAGCATTCAATCTTGGGCGTGTCTTCATCCATTTCTG
tgctaat putative branch site (score: 2)
tttcctatct putative PPT
tatctata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatgaaaatgtttgtggtactttaatcagctagggagtgattagatgaatatgcagcatcacactattgatgctaatgcttcacgtttcctatctatagGTTTTGTTGGGTATGCCATTCTTGTTATCACATCCAGTTGAGTACATCTCACGAGCATTCAATCTTGGGCGTGTCTTCATCCATTTCTG
-catgaaa
- - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - gatgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttca