Sequence
atgc intronic sequence ATGC exonic sequenceAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTgtaagttctttaacttatgagtgtgttgtgttttgttgttctaaaatatccaattagcatctattatattcagccaatattctctaccttcttttttctgttcttcatatttgtcatgaatatttatatttattccataacacttgttcccattcattatattcataagtttatttggtattgtccag
Basic information
species | Glycine max |
transcript | GLYMA09G41160.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41160.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g60700.1 (Oryza sativa), 5'ss of exon 4
AACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTgtaagttctttaacttatgagtgtgttgtgttttgttgttctaaaatatccaattagcatctattatattcagccaatattctctaccttcttttttctgttcttcatatttgtcatgaatatttatatttattccataacacttgttcccattcattatattcataagtttatttggtattgtccag
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AACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGGAAATATCAAATGCATCTGTGgtaagttatgt--tttgaaaatattttagaagatatagtt------------atcagagcccaactcatttgcctgat---ctctttctgtaaattcaagtagtgtgt-tttggcatg----------------------------------------------------------------------
upper sequence: GLYMA09G41160.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G068151_T01 (Zea mays), 5'ss of exon 4
---AACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTgtaagttctttaacttatgagtgtgttgtgttttgttgttctaaaatatccaattagcatctattatattcagccaatattctctaccttcttttttctgttcttcatatttgtcatgaatatttatatttattccataacacttgttcccattcattatattcataagtttatttggtattgtccag
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CTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGA-GATATCTAATGCACCTG--TGgtatgttctta----tatgagtgcaatttagaagtttatgttgtccagcacaacttatgcctcgtttcttt--tcatggttccagacttccaatagtatagtagta----------------------------------------------------------------------------------
upper sequence: GLYMA09G41160.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM5G871928_T01 (Zea mays), 5'ss of exon 2
---AACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTgtaagttctttaacttatg-agtgtgttgtgttttgttgttctaaaatatccaattagcatctattat-attcagccaatattctctaccttcttttttctgttcttcatatttgtcatgaatatttatatttattccataacacttgttcccattcattatattcataagtttatttggtattgtccag
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CTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGA-GATATCTAATGCACCTA--TGgtatgttcttgtatgagtgcaatttagaagtttatgttgtccagcacaacttatgcctcgtttcttttcattggtcccaaacttccaaaagtatagtatt------------------------------------------------------------------------------------------
upper sequence: GLYMA09G41160.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G380227_T01 (Zea mays), 5'ss of exon 3
-AACAGCC--AACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTgtaagttctttaacttatgagtgtgttgtgttttgttgttctaaaatatccaattagcatctattatattcagccaatattctctaccttcttttttctgttcttcatatttgtcatgaatatttatatttattccataacacttgttcccattcattatattcataagtttatttggtattgtccag
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TCTCAACTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGA-GATATCTAATGCACCTG--TGgtatgttcttg----tatgagtgca----atttagaagtt-tatgttgtcca----gcacaacttatgcctcgt-----ttcttttcattggttccaaacttccaaaagtatagtatt----------------------------------------------------------------------
upper sequence: GLYMA09G41160.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM5G828466_T01 (Zea mays), 5'ss of exon 2
---AACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTgtaagttctttaacttatgagtgtgttgtgttttgttgttctaaaatatccaattagcatctattatattcagccaatattctctaccttcttttttctgttcttcatatttgtcatgaatatttatatttattccataacacttgttcccattcattatattcataagtttatttggtattgtccag
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CTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGA-GATATCTAATGCACCTA--TGgtatgttcttg----tatgagtgca----atttagaagtt-tatgttgtcca----gcacaacttatgcctcgt-----ttcttttcattggttccaaacttccaaaagtatagtatt----------------------------------------------------------------------
upper sequence: GLYMA09G41160.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G143790_T01 (Zea mays), 5'ss of exon 2
---AACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTgtaagttctttaacttatgagtgtgttgtgttttgttgttctaaaatatccaattagcatctattatattcagccaatattctctaccttcttttttctgttcttcatatttgtcatgaatatttatatttattccataacacttgttcccattcattatattcataagtttatttggtattgtccag
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CTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGA-GATATCTAATGCACCTG--TGgtatgttcttg----tatgagtgca----atttagaagtt-tatgttgtcca----gcacaacttatgcctcgt-----ttcttttcattggttccaaacttccaaaagtatagtatt----------------------------------------------------------------------
upper sequence: GLYMA09G41160.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G079117_T01 (Zea mays), 5'ss of exon 2
---AACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTg-taagttctttaacttatgagtgtgttgtgttttgttgttctaaaatatccaattagcatctattatattcagccaatattctctaccttcttttttctgttcttcatatttgtcatgaatatttatatttattccataacacttgttcccattcattatattcataagtttatttggtattgtccag
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CTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGA-GATATCTAATGCA---CATGTGgtatgttcttg----tatgagtgca----atttagaagtt-tatgttgtcca----gcacaacttatgcctcgt-----ttcttttcattggttccaaacttccaaaagtatagtatt----------------------------------------------------------------------
upper sequence: GLYMA09G41160.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv08s0058g01290.t01 (Vitis vinifera), 5'ss of exon 4
AACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTgtaagttctttaacttatgagtgtgttgtgtt-ttgttgttctaaaatatccaattagcatctattatattcagccaatattctctaccttcttttttctgttcttcatatttgtcatgaatatttatatttattccataacacttgttcccattcattatattcataagtttatttggtattgtccag
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AACTGCCAATATACAGATTGACAAGGATTTTAGTGCAAAGCTTTCGGGATATGGTTGCGTTGGCCACATTCCAGAAGCAGATGTTTGCAGTAGTTCAGTTgtaagtgctttaactcatatgaggataattctatcattgttttgg--tttccgactgcgagatactactttt--cccatgcatagagatggaatagtacaatca-------------------------------------------------------------------------------------Mapped 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|15203966|gb|BI426743.1|BI426743EST: ATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCT GCTGTTGGAAACCTATCAATGGAAACACTGGAGAAAGGAATGCTCACACCA
genomic: ATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTgtaagttctt ... tattgtccagGCTGTTGGAAACCTATCAATGGAAACACTGGAGAAAGGAATGCTCACACCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAGAGATTTCAAGCAGTTCATCTgtaagttctttaacttatgagtgtgttgtgttttgttgttctaaaatatccaattagcatctattatattcagccaatattctctaccttcttttttctgttcttcatatttgtcatgaatatttatatttattccataacacttgttcccattcattatattcataagtttatttggtattgtccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA