Sequence
atgc intronic sequence ATGC exonic sequencegtcagttcctctgatcaatatccactgcaaaaacaatccgctcgttgcatcagcaaaactctgtaatgagatgactgtctatatgattgtatcacctagGATGTTGATGCTGCAATGAAGAAATCAACTGCAACATGGAAGATAGCTGTAGGACATCATACCATGAGGAGTGTGAGTGCCCATGGAGACACCCAGGAGC
Basic information
species | Oryza sativa |
transcript | LOC_Os10g02750.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g02750.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G152447_T02 (Zea mays), 3'ss of exon 4
gtcagttcctctgatcaatatccactgcaaaaacaatccgctcgttgca--tcagcaaaactctgtaatgagatgactgtctatatgattgt------atcacctagGATGTTGATGCTGCAATGAAGAAATCAACTGCAACATGGAAGATAGCTGTAGGACATCATACCATGAGGAGTGTGAGTGCCCATGGAGACACCCAGGAGC
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-----------------gtgcgcactccgaacacagccatgtcagtgcgggtgaaaggaagctcgttttatagaacctttttttgttgttgttgttctgcgatgcagGATCTGGATGTGGCTATGAAGAAATCAACTGCAAGGTGGAAGATTGTGGTTGGGCATCACACCATGAGGAGTGTGAGTGAGCACAGGGACACCGAGGAGC
upper sequence: LOC_Os10g02750.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G351232_T02 (Zea mays), 3'ss of exon 2
gtcagttcctctgatcaatatccactgcaaaaacaatccgctcgttgcatcagcaaaactctgtaatgagatgactgtctatatgattgtatcacctagGATGTTGATGCTGCAATGAAGAAATCAACTGCAACATGGAAGATAGCTGTAGGACATCATACCATGAGGAGTGTGAGTGCCCATGGAGACACCCAGGAGC
| |||| | || | | || | ||| | || | || | | | || || | ||||| | |||| || ||||||| ||||||||||| |||||||| | || || ||||| ||||||||||||||||||| || || |||||| ||||||
-----------------gtgcgcactccgaacatagtcatattagtgcgggtgaaaggaagctcgttttatagaacttttttttggttctgcattgcagGATATGGATGTGGCTATGAAGAGATCAACTGCAAGGTGGAAGATTGTGGTTGGGCATCACACCATGAGGAGTGTGAGTGAGCACGGGGACACCGAGGAGC
upper sequence: LOC_Os10g02750.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G404769_T01 (Zea mays), 3'ss of exon 10
gtcagttcctctgatcaatatccactgcaaaaacaatccgctcgttgca--tcagcaaaactctgtaatgagatgactgtctatatgattgtatcacctagGATGTTGATGCTGCAATGAAGAAATCAACTGCAACATGGAAGATAGCTGTAGGACATCATACCATGAGGAGTGTGAGTGCCCATGGAGACACCCAGGAGC
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-----------------gtgcgcactccgaacatagtcatattagtgcgggtgaaaggaagctcgtttt-atagaactttttttggttctgcattgc--agGATATGGATGTGGCTATGAAGAGATCAACTGCAAGGTGGAAGATTGTGGTTGGGCATCACACCATGAGGAGTGTGAGTGAGCACGGGGACACCGAGGAGC
upper sequence: LOC_Os10g02750.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AC202435.3_FGT003 (Zea mays), 3'ss of exon 9
gtcagttcctctgatcaatatccactgcaaaaacaatccgctcgttgca--tcagcaaaactctgtaatgagatgactgtctatatgattgtatcacctagGATGTTGATGCTGCAATGAAGAAATCAACTGCAACATGGAAGATAGCTGTAGGACATCATACCATGAGGAGTGTGAGTGCCCATGGAGACACCCAGGAGC
| |||| | || ||| || | ||| | | || || | | | ||| | | | || || | ||||| | |||| || ||||||| ||||||||||| |||||||| | || || ||||| ||||||||||||||||||| || || |||||| ||||||
-----------------gtgcgcactccgaacacagtcatattagtgcgggtgaaaggaagctcgtttt-atagaacttttttttgttctgcattgc--agGATATGGATGTGGCTATGAAGAGATCAACTGCAAGGTGGAAGATTGTGGTTGGGCATCACACCATGAGGAGTGTGAGTGAGCACGGGGACACCGAGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcatcagcaaaactctgtaatgagatgactgtctatatgattgtatcacctagGATGTTGATGCTGCAATGAAGAAATCAACTGCAACATGGAAGATAGCTGTAGGACATCATACCATGAGGAGTGTGAGTGCCCATGGAGACACCCAGGAGC
tatatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttcctctgatcaatatccactgcaaaaacaatccgctcgttgcatcagcaaaactctgtaatgagatgactgtctatatgattgtatcacctagGATGTTGATGCTGCAATGAAGAAATCAACTGCAACATGGAAGATAGCTGTAGGACATCATACCATGAGGAGTGTGAGTGCCCATGGAGACACCCAGGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA