Sequence
atgc intronic sequence ATGC exonic sequence...caacatgagtattgattaattaaagaagaattgagaatgtgatgaattgaagttttgaaaaataccccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g23990.2 |
intron # | 16 |
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 16
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 18
caacatgagtattgattaattaaagaagaattgagaatgt-gatgaattgaagttttgaaaaat-accccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
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ttgtttatttgcacctatgccaaaatatcttttctcttttagatttagtaaagtttctggatttgatttcaattcatcaagttttttacttaaat--cgcagGCTACCATTTATCAACAAAAAGCTTTGGATATCAACGAGAGGGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 18
caacatgagtattgattaattaaagaaga--attgagaatgtgatgaattgaagttttgaaaaat-accccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
| |||| ||| || | ||| | |||| | | ||||| | | | ||| ||| | | || | | ||| ||||||||| || ||||| ||||| || | || ||||| ||||| || | || || ||||| |||||||| |||||||| ||||| ||||||||||| ||||
-atttcagccattgtttatgccaaaatatctattctctttttgatttagtagagtttcaggatttgatttcaattcatcaagttttttacttaaat--cgcagGCTACAATTTATCAACAAAAAGCTTTGGATATCAACGAGAGAGAGTTAGGTCTGGATCATCCTGATACCATGAAGAGCTATGGGGATCTTGCTGTTTTCT
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
caacatgagtattgattaattaaagaagaattgagaatgtgatgaattgaagttttgaaaaataccccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
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--------gtctgtatatattatatgg----ttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattt----tgttaaaa---cagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 3
caacatgagtattgattaattaaagaag---aattgagaatgtgatgaattgaagttttgaaaaataccccaagtcaatatgcttatcatagaaaaaatgca-gGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
||| || || | || | | | | | || || || |||| | | | | || | | | ||| || ||| || || ||||| |||||||| | |||||||||||||| ||||| || || ||||| || || || |||||||||||||||||||||||||||||||
---tatg-gtttttcccatctagggttttccacgtaaatctatgctgtttttttttttttttacttgttgcctattcttaattcaagagttgtcccaattcaagGCCACAATTTATCAACAAAAGGCATTGGACATCAATGAGAGAGAACTAGGACTTGATCATCCAGACACGATGAAGAGTTATGGAGATCTTGCTGTGTTCT
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 18
-caacatgagtat-tgattaattaaagaagaattgagaatgtgatgaattgaagttttgaaaaataccccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
| | | | | | || | || || ||| ||| |||| | | || ||| | | || | ||||| || || ||||| |||||||| | |||||||||||||| ||||| || || ||||| || || ||||||||||||||||||||||||||||||||||
tccatgtaaatctatgctgtttttttttttttttttccttgttgcctattctcatttttccataactatatggttaattcaagagttgtcccaat--ttcagGCCACAATTTATCAACAAAAGGCGTTGGACATCAATGAGAGAGAACTAGGACTTGATCATCCAGACACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
upper sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 17
caacatgagtattgattaattaaagaagaattgagaatgtgatgaattgaagttttgaaaaataccccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
| | | | | | ||| ||||| |||| | || | | | || || || |||||||| ||||| || |||||||| ||||||||||||| | || ||||| | || || || ||||| |||||||| ||||||||||| ||||| || |
-----------------------------gtctgg--tcttgtcacttgcggtttt-----atac----aatctaaacgtttgtc---gacgcttctcagGCTACCATCTACCAACAAAAGGCTTTAGACATCAATGAACGCGAGCTTGGCTTGGACCATCCGGATACCATGAAGAGCTATGGAGATCTGGCTGTCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgaagttttgaaaaataccccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
ttatcatagaaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caacatgagtattgattaattaaagaagaattgagaatgtgatgaattgaagttttgaaaaataccccaagtcaatatgcttatcatagaaaaaatgcagGCTACGATCTATCAGCAAAAGGCCCTAGACATCAATGAGAGGGAACTTGGGCTAGATCACCCTGATACAATGAAGAGTTATGGAGATCTTGCTGTGTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC