Sequence
atgc intronic sequence ATGC exonic sequencegtaaagatatacacatcatactattgataccattagaccatatcttgttgattgaattctctgtgttggtggatctccgaaaccacagctaaccagatctttcatatcatcttctgttaatggtctagATGTGCTTTGATGCGTTTGACGATGCAGCAGATCTTGATGTCTTAGATCATCCAATCCTAAACTTCATATATTACTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G14530.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 10
gtaaagatatacacatcatactattgataccattagaccatatcttgttgattgaattctctgtgttggtggatctccgaaaccacagctaaccagatctttcatatcatcttctgttaatggtctagATGTGCTTTGATGCGTTTGACGATGCAGCAGATCTTGATGTCTTAGATCATCCAATCCTAAACTTCATATATTACTTG
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---------------------gaatggaggtataaaag-atatgt-atctaggaagagaggggtatcaatt-atgtttgcaggtatgtcaaaggaatccgctgacttaagcatgt----atattgcagATGTGCCTTAATGCGTTTGATAAAGCAGCAGATCTTGATGTTCTGAACCATCCAATCCTGAACTTCTTCTATTACCTG
upper sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G28990.1 (Glycine max), 3'ss of exon 9
gtaaagatatacacatcatactattgataccattagaccatatcttgttgattgaattctctgtg-ttggtggatctccgaaaccacagctaaccagatctttcatatcatcttctgttaatggtctagATGTGCTTTGATGCGTTTGACGATGCAGCAGATCTTGATGTCTTAGATCATCCAATCCTAAACTTCATATATTACTTG
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--------------------------------gtgagcccctttttatt--tttaattcttagtgattcctgtttgcttgatttcaaaattga-----------gtttgattgtatgttgttgtatcagATGTGTTTTAATGCATTTGATAAAAATGCGGACCTTGATGTCTTGGATCATCCTATTCTAAACTTCATATATTACCTG
upper sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G01360.1 (Glycine max), 3'ss of exon 9
gtaaagatatacacatcatactattgataccattagaccatatcttgttgattgaattctctgtgttggtggatctccgaaaccacagctaaccagatctttcatatcatcttctgttaatggtctagATGTGCTTTGATGCGTTTGACGATGCAGCAGATCTTGATGTCTTAGATCATCCAATCCTAAACTTCATATATTACTTG
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--------------------------------gtgggcccctttttatt--tttaattcatagtgtttcctgtttgcttggtttcga---aattgagtttg----attgtattttgtt---gtatcagATGTGTTTTAATGCATTTGATAAAAATGCGAACCTTGATGTTTTGGATCATCCTATTCTAAACTTCATATATTACCTG
upper sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 9
gtaaagatatacacatcatactattgataccattagacca-tatcttgttgattgaattctctgtgttggtggatctccgaaaccacagctaaccagatctttcatatcatcttctgttaatggtctagATGTGCTTTGATGCGTTTGACGATGCAGCAGATCTTGATGTCTTAGATCATCCAATCCTAAACTTCATATATTACTTG
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-----------------ataagagtcaaagcacaaaatcagcaccttactg-ctgtatgacatttgtttatcaatat-----attttacctgac-aattttattat-taattttctac--atgac--agATGTGCTTTAATGCGTTTGATCAAGCTGCAAACCTTGATGTTTTGGATCACCCAATTCTAAACTTTATATATTACCTGMapped 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|116477220|gb|EG519812.1|EG519812EST: GCTACGTGACAACCATATGCTTTACATGTTTCCTCATCAGATGTATCATG ATGTGCTTTGATGCGTTTGACGATGCA
genomic: GCTACGTGACAACCATATGCTTTACATGTTTCCTCATCAGATGTATCATGgtaaagatat ... aatggtctagATGTGCTTTGATGCGTTTGACGATGCA
EST:
gi|86076143|gb|DR371900.1|DR371900EST: GCTACGTGACAACCATATGCTTTACATGTTTCCTCATCAGATGTATCATG ATGTGCTTTGATGCGTTTGACGATGCAGCAGATCTTGATGTCTTAGATCAT
genomic: GCTACGTGACAACCATATGCTTTACATGTTTCCTCATCAGATGTATCATGgtaaagatat ... aatggtctagATGTGCTTTGATGCGTTTGACGATGCAGCAGATCTTGATGTCTTAGATCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctccgaaaccacagctaaccagatctttcatatcatcttctgttaatggtctagATGTGCTTTGATGCGTTTGACGATGCAGCAGATCTTGATGTCTTAGATCATCCAATCCTAAACTTCATATATTACTTG
tttcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagatatacacatcatactattgataccattagaccatatcttgttgattgaattctctgtgttggtggatctccgaaaccacagctaaccagatctttcatatcatcttctgttaatggtctagATGTGCTTTGATGCGTTTGACGATGCAGCAGATCTTGATGTCTTAGATCATCCAATCCTAAACTTCATATATTACTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA