Sequence
atgc intronic sequence ATGC exonic sequencegtaagtccctgtggaaatctgatcaagtatgtccattgtcatgatttattctgaagttgtttttggatcgtgcagTTTGAAGATCGCTTCTACATTTACCTGGAATATGTTCACCCAGGTTCAATTAATAAGTATGTCAAACAACATTATGGAGCAATGACGGAATCAGTTGTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os07g02780.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g02780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G20460.1 (Glycine max), 3'ss of exon 5
----gtaagtccctg-----tggaaatctgatcaagt---atgtccattgtcatgatttattctgaagttgtttttggat---cgtgcagTTTGAAGATCGCTTCTACATTTACCTGGAATATGTTCACCCAGGTTCAATTAATAAGTATGTCAAACAACATTATGGAGCAATGACGGAATCAGTTGTCC
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gtaagcaatctcctacttcataattagctgctcaagattaataatcattattctgtaacagccttaaaaccttaacatatgtgcttgcagGTTGAGGACCGGTTTTATATTTATCTGGAATATGTTCATCCTGGTTCAATTAATAAATATGTCCGTGATCATTGTGGTGCCATAACAGAATCTGTCATTC
upper sequence: LOC_Os07g02780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G10050.1 (Glycine max), 3'ss of exon 3
----gtaagtccctg--tggaaat---ctgatcaagt---atgtccattgtcatgatttattctgaagt---------tgtttttggatcgtg------cagTTTGAAGATCGCTTCTACATTTACCTGGAATATGTTCACCCAGGTTCAATTAATAAGTATGTCAAACAACATTATGGAGCAATGACGGAATCAGTTGTCC
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gtaagcaatctcctacttcagaattagctgctcaagattaataatcattattctgtaacagccttaaaaaccttctaacatctttgggttatgtgtttgcagGTTGAGGACCGGTTTTATATTTATCTGGAATATGTTCATCCTGGTTCAATTAATAAATATGTCCGTGAACATTGTGGTGCCATAACAGAATCTGTTATTC
upper sequence: LOC_Os07g02780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------gtaagtccctgtggaa---atctgatcaagtatgtccattgtcatgatttattctgaagttgttt--ttggat-cgtgcagTTTGAAGATCGCTTCTACATTTACCTGGAATATGTTCACCCAGGTTCAATTAATAAGTATGTCAAACAACATTATGGAGCAATGACGGAATCAGTTGTCC
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gtgagtaatcaatctgtttatatatcctctgtttacatatatataatctacctacccaaggcagtgtggc-tgaaaattcattgagcaattctctgattgtgcatgtacagGTAGAAGATCGTTTCTTTATATACCTGGAATATGTTCACCCGGGTTCAATAAACAAATATATCCGTGATCATTGCGGCACCATGACAGAATCTGTTGTTC
upper sequence: LOC_Os07g02780.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s1194g00010.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------gtaagtccctgtggaaatctgatcaagtatgtccattgtcatgatttattctgaagttgtttttggatc-gtgcagTTTGAAGATCGCTTCTACATTTACCTGGAATATGTTCACCCAGGTTCAATTAATAAGTATGTCAAACAACATTATGGAGCAATGACGGAATCAGTTGTCC
| | | ||| | | | | | | | | | | ||| | | |||| | ||||| ||||||| || | || || ||||||||||||||||| || |||||||||||||| |||||| |||||| |||||| || || ||||| ||||| |
gtgagtgatccagttgcagattatggtattcatgcttaacatttgtcttgttagatttccatagtaacttaactgattaatatctcaattttatgcctatgcagGTTGAAGACCGGCTTTATATATACCTGGAATATGTTCATCCTGGTTCAATTAATAAATATGTCCGTGAACATTGTGGAGCTATTACAGAATCTGTTGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcaagtatgtccattgtcatgatttattctgaagttgtttttggatcgtgcagTTTGAAGATCGCTTCTACATTTACCTGGAATATGTTCACCCAGGTTCAATTAATAAGTATGTCAAACAACATTATGGAGCAATGACGGAATCAGTTGTCC
atctgat putative branch site (score: 4)
atgatttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtccctgtggaaatctgatcaagtatgtccattgtcatgatttattctgaagttgtttttggatcgtgcagTTTGAAGATCGCTTCTACATTTACCTGGAATATGTTCACCCAGGTTCAATTAATAAGTATGTCAAACAACATTATGGAGCAATGACGGAATCAGTTGTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA