Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttattttgacttaataaacttcctgatgggtttggtgaatcacttcgacttagaaagtttaaaatacgattagctatagcttttggctatgctaacagtaacattgtcgctttgttgttatgttggcagGTGAATGTGACTGCAGATCATCGCATTGTGTATGGAGCTGACTTGGCTGCTTTTCTCCAAACCTTTGCAAAGATCATTGAGAATCCAGATAGTTTGACCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G25860.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G117786_T01 (Zea mays), 3'ss of exon 5
gtaagttttattttgacttaataaacttcctgatgggtttggtgaatcacttcgacttagaaagtttaaaatacgattagctatagcttttggctatgctaacagtaacattgtcgctttgttgttatgttggcagGTGAATGTGACTGCAGATCATCGCATTGTGTATGGAGCTGACTTGGCTGCTTTTCTCCAAACCTTTGCAAAGATCATTGAGAATCCAGATAGTTTGACCT
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-------------------------ttttctg--gaatttggcta--tggcatagtggacagagtatgaaatgacaacatc-agggcatttg--tat-ttaac--taa-gttgtttcaacattttccttttttcagGTCAATGTCACTGCTGATCACAGGATTGTATACGGTGCTGATTTGGCAGCATTTCTACAAACTTTTGCAAAGATTATTGAGGATCCTGAGAGCTTAACTT
upper sequence: AT3G25860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G24830.2 (Glycine max), 3'ss of exon 5
gtaagttttattttgacttaataaacttcctgatgggtttggtgaatcacttcgacttagaaagtttaaaatacgattagctatagcttttggctatgctaacagtaacattgtcgctttgttgttatgttggcagGTGAATGTGACTGCAGATCATCGCATTGTGTATGGAGCTGACTTGGCTGCTTTTCTCCAAACCTTTGCAAAGATCATTGAGAATCCAGATAGTTTGACCT
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------------------------------tgttatagttag-gagttaggaccatatatggaatcagaattgtttttaa--aagatctctaatcgaattaattggg---tctaaaccctaaacttcctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCTTTCCTCCAGACATTCTCGAAAATCATTGAAAACCCAGAAAGCCTGACAT
upper sequence: AT3G25860.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttttattttgacttaataaacttcctgatgggtttggtgaatcacttcgacttagaaagtttaaaatacgattagctatagcttttggctatgctaacagtaacattg--tcgctttgttgttatgttggcagGTGAATGTGACTGCAGATCATCGCATTGTGTATGGAGCTGACTTGGCTGCTTTTCTCCAAACCTTTGCAAAGATCATTGAGAATCCAGATAGTTTGACCT
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------------------------------------gtctaacttgtcttcttttctggggaggagacaccaaattcttcctaggaattttttttttg-tagcaa-aacactgaactgaattatgaatcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164165613|gb|ES194030.1|ES194030EST: CTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTG GTGAATGTGACTGCAGATCATCGCATTG
genomic: CTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTGgtaagtttta ... atgttggcagGTGAATGTGACTGCAGATCATCGCATTG
EST:
gi|86086933|gb|DR382692.1|DR382692EST: CTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTG GTGAATGTGACTGCAGATCATCGCATTGTGTATGGAGCTGACTTGGCTGCT
genomic: CTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTGgtaagtttta ... atgttggcagGTGAATGTGACTGCAGATCATCGCATTGTGTATGGAGCTGACTTGGCTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatagcttttggctatgctaacagtaacattgtcgctttgttgttatgttggcagGTGAATGTGACTGCAGATCATCGCATTGTGTATGGAGCTGACTTGGCTGCTTTTCTCCAAACCTTTGCAAAGATCATTGAGAATCCAGATAGTTTGACCT
taacatt 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 |
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gtaagttttattttgacttaataaacttcctgatgggtttggtgaatcacttcgacttagaaagtttaaaatacgattagctatagcttttggctatgctaacagtaacattgtcgctttgttgttatgttggcagGTGAATGTGACTGCAGATCATCGCATTGTGTATGGAGCTGACTTGGCTGCTTTTCTCCAAACCTTTGCAAAGATCATTGAGAATCCAGATAGTTTGACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA