Sequence
atgc intronic sequence ATGC exonic sequencegtatcctctttcacaaaacagtctatctttttgaacatttttggatgccatttgttttttaatcactattccaatggatgaatgcagGCTCTTGCTAAACTCATAACAGTTTGTGGTCCCTATCATCGAATGACAGCTGGAGCTTATAGTCTGCTAGCTGTTGTATTGTATCACACTGGTGATTTTA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g23990.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 17
----------------------------gtatcctc---tttcacaaaacagtctatctttttgaacatttttggatgcc-atttgttttttaatcactattccaatggatgaatg-cagGCTCTTGCTAAACTCATAACAGTTTGTGGTCCCTATCATCGAATGACAGCTGGAGCTTATAGTCTGCTAGCTGTTGTATTGTATCACACTGGTGATTTTA
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gtatctacatccagaaccctttgtttggaaatcttcaaattgtggacaaggtttttcaacagtcaacacatttcatttcagaattgttgtgtgatatctgctataattcgttggtgacagGCTCTTGCTAAGCTGGTAGCAGTTTGTGGTCCCTATCATCGGATGACAGCGGGAGCCTACAGCCTCCTTGCTGTAGTTTTATATCATACTGGAGATTTCA
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 17
----------------------------gtatcctct-----ttcacaaaacagtctatctttttgaacatttttggatgccatttgttttttaatcactattccaatggatgaatg-cagGCTCTTGCTAAACTCATAACAGTTTGTGGTCCCTATCATCGAATGACAGCTGGAGCTTATAGTCTGCTAGCTGTTGTATTGTATCACACTGGTGATTTTA
||| || | |||| | | | | | || ||| | | |||| ||| || || | ||| | || |||||||||||||| || || |||||||||||||||||||||| |||||||| ||||| || || || || ||||| || || ||||| ||||| || || |
gtatctacgtccagaaccctttgtttggaaatcttcaaagtgtcgacaaggtttttcaacagtctacac-ctttcatttcagaattgtcgtttgatatctgctataattcgttggtgacagGCTCTTGCTAAGCTGGTAGCAGTTTGTGGTCCCTATCATCGGATGACAGCGGGAGCCTACAGCCTCCTTGCTGTAGTTTTATATCATACTGGAGACTTCA
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 17
---------------gtatcctctttcacaaaacagtctatctttttgaacatttttggatgccatttgttttttaatcactattccaatggatgaatgcagGCTCTTGCTAAACTCATAACAGTTTGTGGTCCCTATCATCGAATGACAGCTGGAGCTTATAGTCTGCTAGCTGTTGTATTGTATCACACTGGTGATTTTA
| | || || | | | | ||| | | | || | |||||| ||| || || | | ||||||||||||||||| || ||||||| ||||||||||| |||||||||| |||||||| ||| | || ||||| || | |||||||||||||| ||||
gtccatgtctactcctcagctatttcttcatattacttgttttttatacagcgtcatgattttgttttgttgttttgtctctttctttttttcctccattagGCTCTTGCTAAACTCGTAGCAGTTTGCGGTCCCTATCACAGAATGACAGCCGGAGCTTACAGTTTACTTGCTGTGGTTCTATATCACACTGGTGACTTTA
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 17
-------------------------------------------------gtatcctctttcacaaaacagtctatcttt--ttgaacatttttggatgccatttgttttttaatcactattccaatggatgaatgcagGCTCTTGCTAAACTCATAACAGTTTGTGGTCCCTATCATCGAATGACAGCTGGAGCTTATAGTCTGCTAGCTGTTGTATTGTATCACACTGGTGATTTTA
||| | || || | ||| ||||| || |||| | || || || | | | |||| ||| | |||||||||| || || || | |||||||||||||||| |||||||||||||| |||||||| || || || ||||| || |||||||| || || || || |
gtatttgatttaaaagtccatcggtttgtcatttctatatgtaaactaccaatcgggtgcagcagaaaaatctttctttgcctgttcattggtaaat-taatatgctacct--tttgtatttttgtggtttt-tgcagGCTCTGGCAAAGCTGGTCGCAGTTTGTGGTCCCTACCATCGAATGACAGCAGGAGCTTACAGCCTCCTTGCTGTAGTTTTGTATCATACAGGGGACTTCA
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------gtatcctctttcacaaaacagtctatctttttgaacatttttggatgccatttgttttttaatcactattccaatggatgaatgcagGCTCTTGCTAAACTCATAACAGTTTGTGGTCCCTATCATCGAATGACAGCTGGAGCTTATAGTCTGCTAGCTGTTGTATTGTATCACACTGGTGATTTTA
||| | | || | ||| ||||| || | | | | | | | | |||| ||| | |||||||||| || || || | |||||||||||||||| ||||||||| |||| |||||||| || || || ||||| || |||||||| || || | || |
gtatttgatttaaaagtccatcggtttgtcatttctatatgtaaactaccaatcgggtgcagtagaaaaatctttctttgcatgttcattggtaaattaat-atgctatcttttgtatttttgtggtttt-tgcagGCTCTGGCAAAGCTGGTCGCAGTTTGTGGTCCCTACCATCGAATGGCAGCAGGAGCTTACAGCCTCCTTGCTGTAGTTTTGTATCATACAGGGAACTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacatttttggatgccatttgttttttaatcactattccaatggatgaatgcagGCTCTTGCTAAACTCATAACAGTTTGTGGTCCCTATCATCGAATGACAGCTGGAGCTTATAGTCTGCTAGCTGTTGTATTGTATCACACTGGTGATTTTA
ttttaat putative branch site (score: 3)
atttgttttttaatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcctctttcacaaaacagtctatctttttgaacatttttggatgccatttgttttttaatcactattccaatggatgaatgcagGCTCTTGCTAAACTCATAACAGTTTGTGGTCCCTATCATCGAATGACAGCTGGAGCTTATAGTCTGCTAGCTGTTGTATTGTATCACACTGGTGATTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT