Sequence
atgc intronic sequence ATGC exonic sequence...taaactttgggtagagtggaaatacattattaccttaaacataatgcagttatgctgataataactaatgtttaatcattatttatgaactggagtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
Basic information
species | Glycine max |
transcript | GLYMA20G39370.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G39370.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g30900.1 (Oryza sativa), 3'ss of exon 3
taaactttgggtagagtggaaatacattattaccttaaacat-aatgcagttatgct--gataataactaatgtttaatcattatttatgaac--tggagtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
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----tattgtgtgagtctaatatgtgattttgaattaagtgtcgatataaatatgtatgaataatgaccg-tactaaacttcaataaattgtttatgtggtatagATCTACCTCCTGATAAGGAAGCATTGGATTGGAACACAAGGATGAAAATTGCGGCTGGTGCTGCTAAGGGACTAGAGTACCTTCATGACAAAGCAAATCC
upper sequence: GLYMA20G39370.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G140095_T03 (Zea mays), 3'ss of exon 3
taaactttgggtagagtggaaatacattattaccttaaacataatgcagttatgctgataataactaatgtttaatcattatttatgaactgg-------agtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
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------tcaaataaa-taaatatataagatattcctccaaacggtgagttcattttgttttgacctgttgatctctcatttgacccaaatggttctacttgatgtagATCTACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTGCAGCAGGTGCTGCCAAAGGACTGGAGTACCTTCATGACAAAGCTAATCC
upper sequence: GLYMA20G39370.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G137468_T02 (Zea mays), 3'ss of exon 2
taaactttgggtagagtggaaatacattattaccttaaacataatgcagttatgctgataataactaatgtttaatca-ttattta--tgaactgg--------agtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
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----------gtaaa-taaatatataagatattcttccaaacagtgcattcattttgttttgatctgtcgaggagtctctcatttgacctaaatggttccacttgatgtagATATACCTCTTGATAAAGAGGCCTTGGACTGGAACACCAGGATGAAAATTGCAGCAGGTGCTGCCAAAGGACTGGAGTACCTACACGACAAAGCTAATCC
upper sequence: GLYMA20G39370.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G015889_T01 (Zea mays), 3'ss of exon 3
taaactttgggtagagtggaaatacattattaccttaaacataatgcagttatgctgataataactaatgtttaatcattatttatgaactgg----------agtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
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------tcattcatattataagcactttgttgcagttaa-gtgttgtagtagtactatcagcag---atgtatattttttatctctgaattaacttagcacttaatgcagATCTCCCTCCTGACAAGGAGCCTTTGGATTGGAACACTAGGATGAAAATTGCTGCGGGTGCTGCTAAAGGGCTGGAGTACCTGCATGACAAGGCACAGCC
upper sequence: GLYMA20G39370.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 3
taaactttgggtagagtggaaatacattattaccttaaacataa-tgcagttatgctgataataactaatgtttaatcattatttatgaac--tggagtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
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---ttgttataatcattacctataaattatacatgtagacttaagttgagaagtagtagttgcttgttttctttggcagcctctaacaaataattttttccagATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAGCTGCTGGTGCGGCGAAAGGATTGGAATTTCTACATGATAAGGCAAACCC
upper sequence: GLYMA20G39370.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0146g00250.t01 (Vitis vinifera), 3'ss of exon 3
taaactttgggtagagtggaaa----tacattattaccttaaacataatgcagttatgctgataataactaatgtttaatcattattta--tgaactggagtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
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----tgcttaataaatttgtaaccattgcctgatcatttcagtcaca-tgagctgttgccaattttagtaacttgtcaaccaatagttaaatgaacttt-gtgcagATCTTCCACCTGATAAGGAACCGCTGGATTGGAACACAAGAATGAAGATAGCAGCTGGTGCAGCCAAGGGTTTGGAATACTTGCATGACAAAGCAAGCCC
upper sequence: GLYMA20G39370.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ23436 (Selaginella moellendorffii), 3'ss of exon 3
taaactttgggtagagtggaaatacattattaccttaaacataatgcagttatgctgataataactaatgtttaatcattatttatgaactggagtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
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----------------------------------------gtttgtctattaatttagttgtttcctgcatacgaaactga---gtgagctttcgtgcagACGTGCCGGCTGACAAGGAACCGTTGGGCTGGAACACAAGGATGAAAATAGCTGCGGGAGCTGCCAGGGGACTGGAGTACCTACATGACAAAGCAAATCC
upper sequence: GLYMA20G39370.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ25419 (Selaginella moellendorffii), 3'ss of exon 3
taaactttgggtagagtggaaatacattattaccttaaacataatgcagttatgctgataataactaatgtttaatcattatttatgaactggagtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
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----------------------------------------gtttgtctattaatttagttgtttcctacatacgaaactga---gtgagctttcgtgcagACGTGCCGGCTGACAAGGAACCGTTGGGCTGGAACACAAGGATGAAAATAGCTGCGGGAGCTGCCAGGGGACTGGAGTACCTGCATGACAAAGCAAATCCMapped 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|14205557|gb|BG839235.1|BG839235EST: CTTAGTTTATGAATTTATGCCTTTTGGATCTTTGGAGGAC-ACCTTCATG ATCTTCCCC-GGACAAGGAACCATTAGATTGGA-CACCAGGATGAAAATAG
genomic: CTTAGTTTATGAATTTATGCCTTTTGGATCTTTGGAGGACCACCTTCATGgtatgtatgc ... tggagtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagttatgctgataataactaatgtttaatcattatttatgaactggagtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
tgataataactaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaactttgggtagagtggaaatacattattaccttaaacataatgcagttatgctgataataactaatgtttaatcattatttatgaactggagtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA