Sequence
atgc intronic sequence ATGC exonic sequence...ttgattagaataagtagcaatatactatactaatagagtgctcagggtttttttttccttcttaatttgattttgcattgaggttgtttcttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA
Basic information
species | Glycine max |
transcript | GLYMA06G30030.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g54760.1 (Oryza sativa), 3'ss of exon 5
ttgattagaataagtagcaatatactatactaatagagtgctcagggtttttttttccttcttaatttgattttgcattgaggttgtttcttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA
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---------gtaatttttaa-atgtt-tagtgatcatgtctacactacgattgattcttttggcacttttttatacactgctactatttttcc-----agACCTACTTGCAATCTATCACTGTGAGGGTTGAGGAATGGAGATTAAAACAAAGAGATACAGAGGAGTGGATGAGGCATCGTCAACTCCCACATGAACTAC
upper sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g38580.3 (Oryza sativa), 3'ss of exon 5
----ttgattagaataagtagcaatatactatactaatagagtgctcagggtttttttttccttcttaatttgattttgcattgaggttgtttcttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA
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aactatcactttgctcataagccattttccacatttgca-accaattgaggttgttggttcagagatgttgcttacttcctttttgtttgtcatctt---gtagACATACTTGCAGTCCATCAGTAAAAGGCTTGAAGAGTGGAGGCTCCGGCAAAGAGATATGGAGGAGTGGATGAGACATCATCAGCTCCCTGATGAACTTC
upper sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g08850.1 (Oryza sativa), 3'ss of exon 5
ttgattagaataagtagcaatatactatactaatagagtgctcagggtttttttttccttcttaatttgattttgcat-tgaggttgtttcttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA
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atgattatactagtaaataccattacaacctcttagcttcaaaggcgtacataattttctttaagaaatattgagctcatcacattatattgtttgc-tagACCTACCTGCAATCTATCACTGCAAGAGTTGAGGAGTGGAGAATAAAGCAAAGAGATACGGAAGAATGGATGAGGCATCGGCAACTTCCTCAGAAACTAA
upper sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G005791_T01 (Zea mays), 3'ss of exon 4
------------------------ttgattagaataagtagcaatatactatactaatag-agtgctca----gggtttttttttccttct----taatttg--attttgcatt----gaggttgtttcttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA
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gtactttttatccactctactgcatactttatattgtacaggctttttatatgtgaacaataatactcgctttggataatttattaattttgacataatttggaattttctgtcttacaacatgatgattattatcaagACCTACCTGCAATCTATTACTGTGAGGGTTGAGGAATGGAGATTAAAGCAAAGAGATACTGAGGAATGGATGAGACATCGTCAGCTTCCTTGTGAACTGC
upper sequence: GLYMA06G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: AT4G30360.1 (Arabidopsis thaliana), 3'ss of exon 4
ttgattagaataagtagcaatatactatactaata-gagtgctcagggttttt-ttttccttcttaatttgattttgcattgaggttgtttcttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA
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-------------gtatggat-tcctgcgttaggataagttctaaaagtatctgcttttgttcttatgtt--tcttgggttttgccttttgtttgt---tagACATATCTGCAATCTTTGACTGTACGGCTTGAGGAATGGAGATTGAAGAAGAGAGACACTGAGGAGTGGATGAGACATCGTCAACTTCCTGAAGAGTTGAMapped 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|7146793|gb|AW508715.1|AW508715EST: TTGCCATCTTGAGTCTTGTATAGATTTCCCATGAGATTGGGAACATGCAG ACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAA
genomic: TTGCCATCTTGGGTCTTGTATTGTTTTCCCATTTGATTGGGAACATGCAGgtatttatgt ... ttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtttttttttccttcttaatttgattttgcattgaggttgtttcttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA
ttgtttctttt CT-rich tract
ttcttaatttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgattagaataagtagcaatatactatactaatagagtgctcagggtttttttttccttcttaatttgattttgcattgaggttgtttcttttgcgtagACATATTTGCAATCAATTACTATAAGGCTTGAGGAGTGGAGGCTTAAGCAAAGAGACACAGAGGAGTGGATGAGGCATCGCCAACTCCCTGAAGATTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - -gagtgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggttg