Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcatgtagtagttttcaatcatggaattgaacagtatctacaaagttgattgtttttttttaccgaagttgttgttgtgtgtatgttgcttttgcagATGGGATTGCCATCAGACAGGGAACAATATATACATAGACTTGGCAGAACTGGGCGGAAAGGTAAGGAAGGAGAAGGTGTACTATTGTTGGCACCGTGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08620.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g43120.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------------------------------gtaaat-catgtagtagt-tttcaatca--tggaattgaacagtatctacaaagtt---gattgtttttttttaccgaagttgttgttgtgtgtatgtt-gcttttgcagATGGGATTGCCATCAGACAGGGAACAATATATACATAGACTTGGCAGAACTGGGCGGAAAGGTAAGGAAGGAGAAGGTGTACTATTGTTGGCACCGTGGG
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gtacctgttattatttcccctcacaaaattcttcttgtaaactgatattgctatattgttgttatttatttttcttttctttatgaatgtttggaaaactatttctgttgaccaaaatatggcaatgcaaatatgcttgcagtttgttgtgttctgataaagttttttctccttgaatatttgctcttgcagGTTGGGGTGCCAGCTGATAGACAGCAATATATACATAGACTTGGTAGAACTGGACGGAAGGGAAAGGAAGGGCAAGGCCTATTACTGTTGGCTCCATGGG
upper sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g43130.1 (Oryza sativa), 3'ss of exon 8
gtaaatcatgtagtagttttcaatcatggaattgaacagtatctacaaagttgattgtttttttttaccgaagttgttgttgtgtgtatgttgcttttgcagATGGGATTGCCATCAGACAGGGAACAATATATACATAGACTTGGCAGAACTGGGCGGAAAGGTAAGGAAGGAGAAGGTGTACTATTGTTGGCACCGTGGG
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------------------gtgggtcgcatgattacatctcatac-caaaataattcatctccatttattgaaatt--tgtt----------tgccctcgcagGTTGGGCTGCCAGCTGATAGAGAACAGTATATACATAGACTTGGTAGAACTGGACGGAAAGGCAAAGATGGGCTAGGTCTCTTACTGTTGGCTCCCTGGG
upper sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g33520.1 (Oryza sativa), 3'ss of exon 8
gtaaatcatgtagtagttttcaatcatggaattgaacagtatctacaaagttgattgtttttttttaccgaagttgttgttgtgtgtatgttgcttttgcagATGGGATTGCCATCAGACAGGGAACAATATATACATAGACTTGGCAGAACTGGGCGGAAAGGTAAGGAAGGAGAAGGTGTACTATTGTTGGCACCGTGGG
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-taaacgttttgttgaaacaaatacgagcatgtgcatattcttttcttttatcatatcctgcttatataccaatgtcagctgattat-cgtcgttattgcagATGGGAGTGCCTACTGACAGAGAACAATATATTCATCGACTTGGTAGAACTGGCCGCAGAGGAAACGAGGGGAGTGGAATCTTATTATTGGCACCGTGGG
upper sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G156158_T02 (Zea mays), 3'ss of exon 8
gtaaatcatgtagtagttttcaatcatggaattgaacagtatctacaaagttgattgtttttttttaccgaagttgttgttgtgtgtatgttgcttttgcagATGGGATTGCCATCAGACAGGGAACAATATATACATAGACTTGGCAGAACTGGGCGGAAAGGTAAGGAAGGAGAAGGTGTACTATTGTTGGCACCGTGGG
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gtgagtcatataattgtgtaccttgccaaaa--gaaaggaaaata-aaagaaaaatgtgtggattcatcaagaaatttatt----------tgcacatgtagGTTGGTCTGCCAGCTGATAGAGAACAGTATATACATAGACTCGGAAGGACTGGACGGAAAGGCAAGGAAGGGCAAGGCATCTTACTACTGGCTCCCTGGG
upper sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv15s0046g01010.t01 (Vitis vinifera), 3'ss of exon 9
------gtaaatcatgtagtagttttcaatcatggaattgaacagtatctacaaagttgattgtttttttttaccgaagttgttgttgtgtgtatgttgcttttgcagATGGGATTGCCATCAGACAGGGAACAATATATACATAGACTTGGCAGAACTGGGCGGAAAGGTAAGGAAGGAGAAGGTGTACTATTGTTGGCACCGTGGG
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ttgaacttgctttatactgtggatttagtataaagatttgag-aatatttcttcagaccgctatgggcttgaaccta----gaaaatatatttctgtaattt---cagGTCGGTTTGCCATCTGATAAAGAACAGTATATACATCGACTTGGTAGAACTGGGCGTAAGGGTAAAGAAGGGCAAGGCATATTGTTACTGGCACCTTGGGMapped 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|124704506|gb|EH795908.1|EH795908EST: ATGTATCTGCTCGTGGTGTTGATTACCCTGATGTGTCCTTAGTCGTACAG ATGGGATTGCCATCAGACAGGGAACAAT
genomic: ATGTATCTGCTCGTGGTGTTGATTACCCTGATGTGTCCTTAGTCGTACAGgtaaatcatg ... gcttttgcagATGGGATTGCCATCAGACAGGGAACAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttgattgtttttttttaccgaagttgttgttgtgtgtatgttgcttttgcagATGGGATTGCCATCAGACAGGGAACAATATATACATAGACTTGGCAGAACTGGGCGGAAAGGTAAGGAAGGAGAAGGTGTACTATTGTTGGCACCGTGGG
agttgat putative branch site (score: 5)
ttgctttt putative PPT
attgttttttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcatgtagtagttttcaatcatggaattgaacagtatctacaaagttgattgtttttttttaccgaagttgttgttgtgtgtatgttgcttttgcagATGGGATTGCCATCAGACAGGGAACAATATATACATAGACTTGGCAGAACTGGGCGGAAAGGTAAGGAAGGAGAAGGTGTACTATTGTTGGCACCGTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
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