Sequence
atgc intronic sequence ATGC exonic sequencegtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttcttttctgttattattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAAGAAAGCAATTGTAGATTCAATTGTGATTCTTATTAGAGATATCCCTGAT
Basic information
species | Glycine max |
transcript | GLYMA12G04820.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 9
gtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagat---gaatggtctaa--attactggtttcttttctgttattattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAAGAAAGCAATTGTAGATTCAATTGTGATTCTTATTAGAGATATCCCTGAT
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----------------------------------gtacgtagaatagcgtatattcttatacagaaatttttaaagatccagaactagcttgtcatcagaacattgaactttgttgt-gtttgcagGATGAACTTTTTGAGTAATATCCTACGGGAAGAGGGTGGCTTTGAGTACAAGAAGGCTATTGTTGATTCAATTATCATACTCATTAGAGATATTCCTGAT
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 9
gtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttcttttctgttattattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAAGAAAGCAATTGTAGATTCAATTGTGATTCTTATTAGAGATATCCCTGAT
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gtatgtatatagaagcgtgtttgcactattcttgtt-----aaacatcgtaaact--------acctttttcatctataagca--------------ttaattttcatttatctgttccagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 9
gtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtcta-aattactggtttcttttctgttattattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAAGAAAGCAATTGTAGATTCAATTGTGATTCTTATTAGAGATATCCCTGAT
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------gtatgtatatagaa----gcatgtcttcttgcgctagtcttgttaaatatcata-aactacctttttca---------tctataagcattaatttccatt----tatctgttttagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGTGGATTCGAGTATAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgttt---ttcctagatgaatggtctaaattactggttt---------cttttctgttattattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAAGAAAGCAATTGTAGATTCAATTGTGATTCTTATTAGAGATATCCCTGAT
|| |||| | | | | | ||| || ||| | || | ||||| |||||||| || | | | || | | | ||| || || | || | |||| ||||||| ||| |||| ||||||||||||||||||||||| ||||| || || | |||||| |||||||| ||||||| |||| |||||||| || |||
gtaagtaaagttttagggtttgttatttgtagttttggtctcgagcatttctatttt-tttgaatgattaaatatgttatggtatctttttagcatttggcttatgattgatctatcaccttttcatttgtagGATGACCTTCTTAAGCAACATTCTTAGGGAAGAAGGTGGATTTGAGTATAAAAGAGCAATAGTAGATTCTATTGTGACCATTATCAGAGATATTCCGGAT
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 9
gtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttc------------------ttttctgttattattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAAGAAAGCAATTGTAGATTCAATTGTGATTCTTATTAGAGATATCCCTGAT
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------gtaagt-gatatcctgtttttgatgtcat--cattaaaacatttgggttttatttttatgtcttttttaaatgaacagtgtaaaatgtttccgtcatgtgaaatagaataaccctttttcccttgcttttcagGATGAACTTCTTAAGCAACATTCTTAGGGAAGAAGGTGGATTTGAGTACAAAAAGGCGATTGTTGATTCAATCGTGATCCTCATAAGAGATATTCCTGATMapped 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|208300498|gb|GE100263.1|GE100263EST: CAATAAGATCTACTATGCTTGAAATTCCCTTTAAAATATAGATCTCT GATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAA
genomic: CAATAAGATC-ACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtatat ... ttattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttcctagatgaatggtctaaattactggtttcttttctgttattattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAAGAAAGCAATTGTAGATTCAATTGTGATTCTTATTAGAGATATCCCTGAT
gtctaaa putative branch site (score: 3)
tttcttttctgttatt putative PPT
tttcttttctgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtatatgtcaatgtcattctataggtttctttcccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttcttttctgttattattttcagGATGAATTTCCTAAGTAACATTCTTAGGGAAGAAGGTGGCTTTGATTACAAGAAAGCAATTGTAGATTCAATTGTGATTCTTATTAGAGATATCCCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA