Sequence
atgc intronic sequence ATGC exonic sequence...ttgtaattgttcagatgaagtttggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG
Basic information
species | Glycine max |
transcript | GLYMA08G20900.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 11
ttgtaattgttcagatgaagtttggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG
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------------gcaagaacctaaatattttcttgattatattatctcttattttat-----tcagaaattataagtatgccaa----ttctgtgttcagGTACTTGACTGTGCAGTTTGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAGAAGGCAAAGATTTTACGG
upper sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G028733_T02 (Zea mays), 3'ss of exon 12
ttgtaattgttcagatgaagtttggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG
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-----gtaagtccattaaatctttgcatttcacttgtgtcctcgtttatacagtgtcctcatttatacagaaaaaaaatacataatactccttcctttagGTACTTGACTGTGCAGTTCGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCGAAGATTTTACGA
upper sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 11
ttgtaattgttcagatgaagtttggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG
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----------------gcaagtacattaaatctttgc-atttcacttgt-cctcgttaat-acagcaaaaaaagtaatattc-----cttccttt---agGTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA
upper sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 11
-ttgtaattgttcagatgaagtttggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG
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tgtggagtctactggcacccttctttttctatctccttgcttttgtttgtatatttctgggtgaagaaagaga-attcttacaaataattttttcttctagGTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG
upper sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ12930 (Selaginella moellendorffii), 3'ss of exon 10
ttgtaattgttcagatgaagtttggttgtttctttgt-tgtgttatttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG
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-----------------------------------gtacgtgggttttatgatttatcaattgctctaaatg---------tgcactgttttgttc---agATACTTGACTGTGCAGTTTGTTCGTTTCTTCTGGAAGCGGGAAACGAAACAGAAAGCAAAGATCTTGAGGMapped 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|13789583|gb|BG652174.1|BG652174EST: GGCCGTAGTGCTACATACTTGAAGGAATCACGCATCAATGCCTTGCCAAG GTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCA
genomic: GGCCGTAGTGCTACATACTTGAAGGAATCACGCATCAATGCCTTGCCAAGgttgatattc ... ccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCA
EST:
gi|17022113|gb|BM093147.1|BM093147EST: GGCCGTAGTGCTACATACTTGAAGGAATCACGCATCAATGCCTTGCCAAG GTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCA
genomic: GGCCGTAGTGCTACATACTTGAAGGAATCACGCATCAATGCCTTGCCAAGgttgatattc ... ccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG
ttttcaaccttttcct CT-rich tract
atatgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtaattgttcagatgaagtttggttgtttctttgttgtgttatttcttccttggtaattgctatgagtgatatgattttcaaccttttccttttcaagGTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - -ggttgtt
- - - - - - - - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacctt