Sequence
atgc intronic sequence ATGC exonic sequence...tatttagtcaaattcatggggatttttactttttgagtttaacttatggtgtttttttaagtaaattttgtggtgacattcttggtggttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACAAGGAAAGGACGACAAG
Basic information
species | Glycine max |
transcript | GLYMA0041S00200.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g56050.1 (Oryza sativa), 3'ss of exon 2
----tatttagtcaaattcatggggatttttactttttg--agtttaac-ttatggtgtttttttaagtaaattt-tgtggtgacattcttggtggttgtgta---tgcagGCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACAAGGAAAGGACGACAAG
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gtagtagctag-cagcgccatagtgacagacacctctcgccaccatgccgccatggcttccaccttcacagcttcacttaacctcaagtaaaaaaaccttgtaaaaagcagGCATAGGTGGACTGGGAGATATGAGGCACACCTCTGGGACAACAGCTGCAAGAAGGAAGGCCAGACCAGAAAAGGACGCCAAG
upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 2
tat-ttagtcaaattcatggggatttttactttttgagtttaacttatggtgtttttttaagtaaattttgtggtgacattcttggtgg--ttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACAAGGAAAGGACGACAAG
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tgtattgatgaggcacctac---tcttttgtttttgagcaaatcatttgaccctttttatattgaatgacgaaggtttgtgtgtgtttgattcactggagcagGCACAGGTGGACTGGAAGATATGAAGCCCACCTCTGGGATAACAGTTGCAAAAAGGATGGACAGACAAGGAAGGGAAGGCAAG
upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 2
tatttagtcaaattcatggggatttttactttttgagtttaacttatggt--gtttttttaagtaaattttgtggtgacattcttggt-ggttgtgt-atgcagGCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACAAGGAAAGGACGACAAG
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----------------gttgtttttttattttataatattaaactttgtttgactttcgttagtaa-tgttacatatacttacttaaaaggttatgtgaaacagACATAGATGGACTGGTAGATATGAAGCTCATCTATGGGACAATAGTTTCAAGAAGGAAGGTCACAGTAGAAAAGGAAGACAAG
upper sequence: GLYMA0041S00200.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------------------------------------tatttagtcaaattcatggggatttttactttttgagtttaacttatggtgtttttttaagtaaattttgtggtgacattcttggtggtt-gtgtatgcagGCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACAAGGAAAGGACGACAAG
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gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAGMapped 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|207752986|gb|GD725524.1|GD725524EST: TCCATCGACACATTTGGTCAAAGAACTTCTCAGTATAGAGGTGTCACAAG GCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTG
genomic: TCCATCGACACATTTGGTCAAAGAACTTCTCAGTATAGAGGTGTCACAAGgttagtactt ... gtgtatgcagGCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggtgtttttttaagtaaattttgtggtgacattcttggtggttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACAAGGAAAGGACGACAAG
tttttttaagtaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttagtcaaattcatggggatttttactttttgagtttaacttatggtgtttttttaagtaaattttgtggtgacattcttggtggttgtgtatgcagGCATAGATGGACTGGTAGATATGAAGCACATTTGTGGGATAACAGTTGCAAGAAGGAAGGGCAAACAAGGAAAGGACGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - ttcatgg
- - - - - - - - - - - - - - - - - - - - - cttatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtggt