Sequence
atgc intronic sequence ATGC exonic sequencegtacgtctttgatcttacaaagttgatctgagaaaccatctatacaatttatctgatgttgacatgctacatgtaacccatgaaatatcactaacagttaccgggaacattgttttgcagTTTCGTTTCAGCTATATGATCTTAAGCAGCAAGGTTTCATAGAGAGGCAAGAGGTGAAGCAAATGGTGGTGGCTACTCTTGCTGAGTCCGGCATGAACCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26570.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 7
gtacgtctttgatcttacaaagttgatctgagaaaccatctatacaatttatctgatgttgacatgctacatgtaacccatgaaatatcactaacagttaccgggaacattgttttgcagTTTCGTTTCAGCTA-TATGATCTTAAGCAGCAAGGTTTCATAGAGAG-GCAAGAGGTGAAGCAAATGGTGGTGGCTACTCTTGCTGAGTCCGGCATGAACCT
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-tacttattcgtttttg--gatttaattctaaattttgttt------ctcgtttgagacaagcctgttttttgtatggctttcaatat-------aggTGAAGCAAATGGTAGTTGCTACTCTTGCTGAATCTGGCATGAACCTATCAGATGACGTT--ATAGAAAGTATAATTGACAAGG-----------------------------------------
upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 6
gtacgtctttgatcttacaaagttgatctgagaaaccatctatacaatttatctgatgttgacatgctacatgtaacccatgaaatatcactaacagttaccgggaacattgttttgcagTTTCGTTTCAGCTA-TATGATCTTAAGCAGCAAGGTTTCATAGAGAGGCAAGAGGTGAAGCAAATGGTGGTGGCTACTCTTGCTGAGTCCGGCATGAACCT
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----gtacttagtcatctttgatttaattctaaat---tttttgctcctcatttgagacaagcctgatttttgta-----tgactttcta--aatagGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTAT-CAG-ATGATGTTATAGAAAGTATAATTGACAAG-----------------------------------------
upper sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 5
---------------------gtacgtctttgatctta---caaagttgatctgagaaaccatc-----tatacaattta--tctgatgttgacatgctacatgtaacccatgaaatatcactaacagtta----ccgggaacattgttttgcagTTTCGTTTCAGCTATATGATCTTAAGCAGCAAGGTTTCATAGAGAGGCAAGAGGTGAAGCAAATGGTGGTGGCTACTCTTGCTGAGTCCGGCATGAACCT
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gtatgttgtacaatattttttctacaattattattttagcatacagattttctgtaaatttaataacaatgcacaattgaaatcaagtctttaattttctttgataacctttttaa-ataaacaaaaattgaacccatgtgatatcatgtttcagTTTCCTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGGCAAGAG-----------------------------------------------Mapped 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|86076567|gb|DR372324.1|DR372324EST: TGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACAAGATTGACT TTTCGTTTCAGCTATATGATCTTAAGCAGCAAGGTTTCATAGAGAGGCAAG
genomic: TGCTCTCTCTGTCTTTCATCCAAATGCTCCCATAGAAGACAAGATTGACTgtacgtcttt ... tgttttgcagTTTCGTTTCAGCTATATGATCTTAAGCAGCAAGGTTTCATAGAGAGGCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctacatgtaacccatgaaatatcactaacagttaccgggaacattgttttgcagTTTCGTTTCAGCTATATGATCTTAAGCAGCAAGGTTTCATAGAGAGGCAAGAGGTGAAGCAAATGGTGGTGGCTACTCTTGCTGAGTCCGGCATGAACCT
cactaac putative branch site (score: 1)
ttgtttt putative PPT
atgaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtctttgatcttacaaagttgatctgagaaaccatctatacaatttatctgatgttgacatgctacatgtaacccatgaaatatcactaacagttaccgggaacattgttttgcagTTTCGTTTCAGCTATATGATCTTAAGCAGCAAGGTTTCATAGAGAGGCAAGAGGTGAAGCAAATGGTGGTGGCTACTCTTGCTGAGTCCGGCATGAACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG