Sequence
atgc intronic sequence ATGC exonic sequence...tccagattcaaatttattaaattcctactcaacctttccaacctggttgccttaccgtctcatctgttactgagctaatatggtctgaacttcttattagGTTCACCGAGTGCTTGTTGACATAGTTTCAGCTTCCGCGAATGCCACACCTGGTCTTGGGAGATATCCTCCTTTTAAGAGAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G59610.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 10
tccagattcaaatttat-taaattcctactcaacctttccaacctggttgccttac-cgtctcatctgttactgagctaatatggtctgaacttcttattagGTTCACCGAGTGCTTGTTGACATAGTTTCAGCTTCCGCGAATGCCACACCTGGTCTTGGGAGATATCCTCCTTTTAAGAGAGAG
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-gaagttctttgtgtgtatacatagtgaagtaatactatatatatagttttagtgcacatcttgcctctttccacaggaaactaatttgacattca-attagGTTCATCGTGTATTGTTAGACATAGTCAATGCTTCCGCAAATGCCACACCAGGACTTGGGAGATATCCTCCATTCAAGCGTGAG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 10
tccagattcaaatttattaa-attcctactcaacctttccaacctggttgccttacc--gtctcatctgttactgagctaatatggtctgaacttctta--ttagGTTCACCGAGTGCTTGTTGACATAGTTTCAGCTTCCGCGAATGCCACACCTGGTCTTGGGAGATATCCTCCTTTTAAGAGAGAG
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---aactttgtaatcattattattatgaatagatcactctg--ctgagtggtatacttgagcaaattcagaaaataaattctttgtttctttcttctcacattagGTACATCGCGTGCTTGTGGATCTTGTTTCTGCTTCTGCAAATGCAACGCCTGGTCTTGGAAGGTATCCTCCATTCAAGAGAGAG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 10
tccagattcaaatttattaa--attcctactcaacctttccaacctggttgccttaccgtctcatctgttactgagctaatatggtctgaacttcttattagGTTCACCGAGTGCTTGTTGACATAGTTTCAGCTTCCGCGAATGCCACACCTGGTCTTGGGAGATATCCTCCTTTTAAGAGAGAG
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-tgtactgcatgttcttctatgattttttctaaacatgtagcttcttgctgtattttgcttatgccaccctttaagctcac-tattattgttgccaaaatagGTGCACCGTGTGCTTGTTGACATAGTCTCTGCTGCTGCAAATGCTACACCGGGCCTGGGAAGATACCCTCCTTTTAAGAGAGAG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 10
tccagattcaaatttatta---aattcctactcaacctttccaacctggttgccttaccgtctcatctgttactgagctaatatggtctgaacttcttattagGTTCACCGAGTGCTTGTTGACATAGTTTCAGCTTCCGCGAATGCCACACCTGGTCTTGGGAGATATCCTCCTTTTAAGAGAGAG
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ttgaattttccctttgttatttgatgtctatgtggcccattgaatggaattctttaaccacctactgtgtttgttgcatactgatgactatgaaaca---tagGTGCACCGTGTCCTGGTAGATGTAGTTTCTGCTGCTGCAAATGCTACGCCAGGTCTGGGGAGATATCCTCCTTTCAAGAGAGAGMapped 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|125050910|gb|EL123179.1|EL123179EST: CTTGAGTTGGCTAAAGACCCAGCACGACTATGTGTTGATGAG GTTCACCGAGTGCTTGTTGACATAGTTTCAGCTTCCGCGAA
genomic: CTTGAGTTGGCTAAAGACCCAGCACGACTATGTGTTGATGAGgtgtgtccat ... ttcttattagGTTCACCGAGTGCTTGTTGACATAGTTTCAGCTTCCGCGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgccttaccgtctcatctgttactgagctaatatggtctgaacttcttattagGTTCACCGAGTGCTTGTTGACATAGTTTCAGCTTCCGCGAATGCCACACCTGGTCTTGGGAGATATCCTCCTTTTAAGAGAGAG
agctaat putative branch site (score: 3)
cttcttatt putative PPT
ttcttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccagattcaaatttattaaattcctactcaacctttccaacctggttgccttaccgtctcatctgttactgagctaatatggtctgaacttcttattagGTTCACCGAGTGCTTGTTGACATAGTTTCAGCTTCCGCGAATGCCACACCTGGTCTTGGGAGATATCCTCCTTTTAAGAGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - -attcaaa
- - - - - - - - - - - - - -ctcaacc
- - - - - - - - - - - - - - - - - - -ccaacct