Sequence
atgc intronic sequence ATGC exonic sequence...gcttttgtttgaacacatggatttctgaagacctctacatataatgcttctgcaactgttacctctgattttgttgtgatttattatctaatttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
Basic information
species | Glycine max |
transcript | GLYMA10G44050.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 12
---gcttttgtttgaacacatggatttctgaagacctctacatataatgcttctgca-actgttacctctgattttgttgtgatttattatctaatttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
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ggtcctttttcttttccgaatgtagaccctgtcacgattgtgcgt----ctttgacagattagtttttttgttggtcctctgatatagtatgtttgatggccagGCACACCATATACACAGCAATCTTATAAAGTCAGTGATTCCTTTCCATTTAAGTGGATAAACAAGAAATGGAAAGAAGGTTTTCATGTGACTGCAATGGC
upper sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 13
gcttttgt-ttgaacacatggatttctgaagacctctaca--tataatgcttctgcaactgtt--acctctgattt-tgttgtgatttattatctaat---ttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
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gtatctacacttttcatgaatacttttgaacactttcgtcattatggtattttactagtctctgaatttgtggcttattctatgtttggttttcaaatgaattatgaagGTACGCAGTATACACAGCAGTCTTACAAAGTAAGCGATTCATTCCCGTTCAAGTGGATAAACAAGAAATGGAGAGAAGGCTTCCATGTAACCTCAATGGC
upper sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 13
--gcttttgtttgaacacatggatttctgaagacctctacatataatgcttctgcaactgttacctctgattttgttgtg-atttattatctaatttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
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acctatttacatgaagacactgattat--gagtccccagttgctaat-ttatggtagttattttcagccactttatcatttgaccataaccaaatatctgcagGCACACAATATACTCAACAGTCTTACAAAGTAAGCGACTCCTTTCCCTTTAAATGGATAAACAAGAAGTGGAGAGAAGGATTCCATGTAACTTCCATGGC
upper sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gcttttgtttgaacacatggatttctgaagacctctacatataatgcttctgcaactgtta-cctctgattttgttgtgatttattatctaatttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
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----------------------------------------gtattgtcgctgttattgatggccactggcattgtcgctgacgcgtgttt--cccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC
upper sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gcttttgtttgaacacatggatttctgaagacctctacatataatgcttctgcaactgtta-cctctgattttgttg-tgatttattatctaatttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
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----------------------------------------gtattgtcgctgttattgatggccactggcattgttgctgacgcgtgattc---ccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGCMapped 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|58019825|gb|CX706567.1|CX706567EST: TTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAG GTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCA
genomic: TTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAGgtttgattac ... atttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttctgcaactgttacctctgattttgttgtgatttattatctaatttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
atctaat putative branch site (score: 3)
tttttgc CT-rich tract
attttgttgtgattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttttgtttgaacacatggatttctgaagacctctacatataatgcttctgcaactgttacctctgattttgttgtgatttattatctaatttttgcagGTACGCAGTATACTCAACAATCCTACAAAGTGAGTGAATCTTTCCCCTTCAAATGGATAAACAAGAAGTGGAGAGAAGGTTTTCATGTCACTTCAATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
gcttttg
- - - - - -aacacat
- - - - - - - - - - - - - - - - ctctaca
- - - - - - - - - - - - - - - - - - - - - - - cttctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtg