Sequence
atgc intronic sequence ATGC exonic sequencegtgaggaaatacattatcgatcttcatgcagcttagtaatttcagttgcttctagtgcggttgacttagcgtggttgtctatcttgtacagGATTTCGTGATTCTATAGATGACAAGTCGAAGGCTAATGTGGTTCAAATCAAAGGAAGATTTTCAGTAACATCAGAAAACTTGGATCTTGCAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G10730.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G10730.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 10
--------gtgaggaaatacattatcgatcttcatgcag--cttagtaattt-cagttg--cttctagtgcggttgacttag--cgtggttgtctatcttgtac-agGATTTCGTGATTCTATAGATGACAAGTCGAAGGCTAATGTGGTTCAAATCAAAGGAAGATTTTCAGTAACATCAGAAAACTTGGATCTTGCAAGG
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gtatttgaatcatcatgtacaccgtaaggctgtgtgcaagttttagtatttttcaaccagccatcttaaacacttggttttgattttgttcacccaactcctgctagGATTCAGAGATTCCTTGGATGATAAGTCTAAGGCTAATCTAGTGCAAATTAAAGGACGATTTTCAGTGACATCAGAAAATTTAGATCTGGTGAAG
upper sequence: AT4G10730.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G31630.3 (Glycine max), 3'ss of exon 10
--------gtgaggaaatacattatcgatcttcatgc--agcttagtaatttc--agttgcttctagtgcggttgacttag--cgtggttgtctatcttgtac-agGATTTCGTGATTCTATAGATGACAAGTCGAAGGCTAATGTGGTTCAAATCAAAGGAAGATTTTCAGTAACATCAGAAAACTTGGATCTTGCAAGG
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gtatttgaatcatcatgtacaccgtaaggctgtgtgctagttttagtatttttcaaccagcctcttaaacacttggttttgattttgttcacccaactcttgctagGATTCAGAGATTCCTTGGATGATAAGTCTAAGGCTAATCTAGTGCAAATTAAAGGACGATTTTCAGTGACATCAGAAAATTTAGATCTGGTGAAG
upper sequence: AT4G10730.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA20G16510.2 (Glycine max), 3'ss of exon 11
---gtgaggaaatacattatcgatcttcatgc--agcttagtaatttcagttgcttctagtgcgg------ttgact-------tagcgtggttgtc--tatcttgtacagGATTTCGTGATTCTATAGATGACAAGTCGAAGGCTAATGTGGTTCAAATCAAAGGAAGATTTTCAGTAACATCAGAAAACTTGGATCTTGCAAGG
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gtacttaaattatactgtgtgaaccataaagctatgtgcagaatttctactagtttttgaaccaaacaatcttaactctgactttaatttggttcccatcactcttggtagGATTCAGAGATTCCTTGGATGACAAGTCTAAGGCTACTCTTGTGCAAATTAAAGGGCGATTCTCTGTAACATCAGAAAATTTAGATCTTGTGAAG
upper sequence: AT4G10730.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA13G10450.2 (Glycine max), 3'ss of exon 11
----------------------gtgaggaaatacattatcgatcttcatgcagcttagtaatttcagttgcttctagtgcggttgacttagcgtggttgtc--tatcttgtacagGATTTCGTGATTCTATAGATGACAAGTCGAAGGCTAATGTGGTTCAAATCAAAGGAAGATTTTCAGTAACATCAGAAAACTTGGATCTTGCAAGG
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gtacttaaattatactgtatgaaccataaggctatgtgtagaatttgtactagtttcttaac--caaaccatcttaattctttgagtttaatttggttcccatcactcttgatagGATTCATAGATTCCTTGGATGACAAGTCTAAGGCTAATCTAGTGCAAATTAAAGGGCGATTCTCTGTGACATCAGAAAATTTAGATCTTGTGAAGMapped 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|86059749|gb|DR355506.1|DR355506EST: AAATCGTGCTTCAGCAAACAGTCTTTCAGCTCCTATCAAATCTTCTGGAG GATTTCGTGATTCTATAGATGACAAGTCGAAGGCTAATGTGGTTCAAATCA
genomic: AAATCGTGCTTCAGCAAACAGTCTTTCAGCTCCTATCAAATCTTCTGGAGgtgaggaaat ... tcttgtacagGATTTCGTGATTCTATAGATGACAAGTCGAAGGCTAATGTGGTTCAAATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatttcagttgcttctagtgcggttgacttagcgtggttgtctatcttgtacagGATTTCGTGATTCTATAGATGACAAGTCGAAGGCTAATGTGGTTCAAATCAAAGGAAGATTTTCAGTAACATCAGAAAACTTGGATCTTGCAAGG
ggttgac putative branch site (score: 4)
tctatctt putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggaaatacattatcgatcttcatgcagcttagtaatttcagttgcttctagtgcggttgacttagcgtggttgtctatcttgtacagGATTTCGTGATTCTATAGATGACAAGTCGAAGGCTAATGTGGTTCAAATCAAAGGAAGATTTTCAGTAACATCAGAAAACTTGGATCTTGCAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA