Sequence
atgc intronic sequence ATGC exonic sequencegtatatatactgcgtgatcaagatcatgccttcttcttcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcatatatactgcgtagtactacattaattcttcttttggttgagatgcaaatcaacaaattaattaagatgaattattgcagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os05g48850.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g48850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G031200_T02 (Zea mays), 3'ss of exon 1
gtatatatactgcgtgatcaagatcatgccttcttct-tcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcatat-atactgcgta-gtactacattaattctt-cttttggttgagatg-caaatcaacaaattaattaagatgaattattg----cagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC---
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--gtacatactacgttg-cgtacgcacgcgcgcgtcgatcgtgtgggcgtgcatgcatgttagcttggtggtgctgggctagctagctcttctcgtccatgtcatgactcatgcatgcagttatatagcttgctgatgatcgacatgatcgatcgatgaacaaactgatattatataatgtggtcagaagAGCACGACGATCCAGGACTTGCCGGGGCTGCCGGCCGGCGTGAAGTTCGACCCGACGGACCAGGAGCTGCTGGAGCACTTGGAGGGGAAGGCGAGGCCGG
upper sequence: LOC_Os05g48850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G031200_T01 (Zea mays), 3'ss of exon 1
gtatatatactgcgtgatcaagatcatgccttcttct-tcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcatat-atactgcgta-gtactacattaattctt-cttttggttgagatg-caaatcaacaaattaattaagatgaattattg----cagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC
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--gtacatactacgttg-cgtacgcacgcgcgcgtcgatcgtgtgggcgtgcatgcatgttagcttggtggtgctgggctagctagctcttctcgtccatgtcatgactcatgcatgcagttatatagcttgctgatgatcgacatgatcgatcgatgaacaaactgatattatataatgtggtcagAAGAGCACGACGATCCAGGACTTGCCGGGGCTGCCGGCCGGCGTGAAGTTCGACCCGACGGACCAGGAGCTGCTGGAGCACTTGGAGGGGAAGGCGAGGC
upper sequence: LOC_Os05g48850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G36980.1 (Glycine max), 3'ss of exon 1
gtatatatactgcgtgatcaagatcatgccttcttcttcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcatatatactgcgtagta-ctacattaattcttcttttggttgagatgcaaatcaacaaattaattaagatgaattattgcagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC---
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---------------------------------------------------------------------------acctaacgaattgtatctaacttttgtctttatattttttctattttattggggcattcatttcaagaataaacatctatatt--ttggtattaattctt-----agGCTGCTGGAATTCATGACTTGCCTGGACTTCCTGCTGGAGTGAAGTTTGATCCTACTGATCAGGAGATTCTTGAACATTTGGAAGCGAAGGTGCGCTCTG
upper sequence: LOC_Os05g48850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA12G33460.1 (Glycine max), 3'ss of exon 1
gtatatatactgcgtgatcaagatcatgccttcttcttcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcatatatactgcgtagtactacattaattcttcttttggttgagatgcaaatcaacaaattaattaagatgaattattgcagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC---
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--------------------------------------------------------------------------aatt--atagctaagttttgtctttattttttctattttattagatttggggcattcatttcaagaatatatatatatattttttttggtattaattttt-----agGCTGCTGGAATTCATGACTTGCCTGGACTTCCTGCTGGAGTGAAGTTTGATCCTACTGATCAGGAGATTCTTGAACATTTGGAAGCGAAGGTGCGCTCTG
upper sequence: LOC_Os05g48850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv10s0003g00350.t01 (Vitis vinifera), 3'ss of exon 2
gtatatatactgcgtgatcaagatcatgccttcttcttcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcatatatactgcgtagtactacattaattcttcttttggt-tgagatgcaaatcaacaaattaattaagatgaattattgcagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC------
| | || || | || || ||| || | | | | | | || || || ||| | | |||||| | | | | ||| || || | ||||| ||||| || |||||||||||||||||||| ||||| ||| ||||||| || || || | |||| | |
-----------------------------------------------------------------------------------------gttttttttctcatgctatcttttatta-attgttttgtgctgtattatttggtgttgattttcatgttag--acggacaattatacttgaatcagGCCGGGATTCATGATTTACCGGGACTGCCTGCGGGAGTGAAGTTCGATCCGACAGACCAAGAGATTCTTGAACACTTAGAGGCAAAGGTGCTGTCTGATA
upper sequence: LOC_Os05g48850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv12s0028g03050.t01 (Vitis vinifera), 3'ss of exon 1
gtatatatactgcgtgatcaagatcatgccttcttcttcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcat-atatac-tgcgtagtactacattaattctt----cttttggttgagatgca--aatcaacaaattaattaagatgaattattgcagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC------
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gttgattaattcccatgcacagaattttcttccttttcttttttggtttttgcaaatgat-gtcatgatttttccctttttctttttaggtctaattgttatttaaatgccaagaactgcttttgctattgatactatgagtttctttttctcacttgtgtcattgtttaattttgaattaaaaaaaaaaagGCTCGAATTCATGATCTGCCAGGGCTACCGGCCGGAGTGAAGTTCGATCCGACTGATCAGGAGCTTCTTGAACATTTAGATGGGAAGGTGAGGTGTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttcttttggttgagatgcaaatcaacaaattaattaagatgaattattgcagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC
aattaat putative branch site (score: 3)
aaatcaacaaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatatactgcgtgatcaagatcatgccttcttcttcttctttttttctgaatgcaacagccaacagctataaattcagcaagtgataactgatcatatatactgcgtagtactacattaattcttcttttggttgagatgcaaatcaacaaattaattaagatgaattattgcagGAGACGACGACGATCCAGGACCTGCCGGGGCTGCCGGCCGGAGTGAAGTTCGATCCGACGGACCAGGAGCTTCTTGAGCATTTGGAAGGGAAGGCGAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG