Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttaaaatgcactcttcagcagtgatgagttccttttgtttgcgtgtgttttaaatatatgattttactttgtgaaaggatgcctcattgcctcttatttcaactgtataaagcccatgtgaattattcaatatattttactgaatatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGCG
Basic information
species | Glycine max |
transcript | GLYMA05G31080.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G31080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g26914.2 (Oryza sativa), 3'ss of exon 3
gtaagtttaaaatgcactcttcagcagtgatgagttccttttgtttgcgtgtgttttaaatatatgattttactttgtgaaaggatgcctcattgcctcttatttcaactgtataaagcccatgtgaattattcaatatattttactga-atatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGCG
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-------------------------------------------------------------------------------gtgagttacttcatttgcttttctt----ctttgctggtattattagaa------aatccagtttcctgacatggatttgatattttaatttacagGATTTCTATTCCACACTTGGTGTTTCAAGAAATGCTAGTAAATCTGAAATCAAGAGTG
upper sequence: GLYMA05G31080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G091811_T01 (Zea mays), 3'ss of exon 3
gtaagtttaaaatgcactcttcagcagtgatgagttccttttgtttgcgtgtgttttaaatatatgattttactttgtgaaaggatgcctcattgcctcttatttcaactgtataaagcccatgtgaattattcaatatattttactgaatatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGCG
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----------------------------------------------------------------------------gtgagctattcttttgt--cttcctgttttgcttacattattgcttcaaaatgtcttccgt---tcttacttgga----tttaaatatcaaatgacagGATTTCTATAACGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG
upper sequence: GLYMA05G31080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G856084_T01 (Zea mays), 3'ss of exon 3
gtaagtttaaaatgcactcttcagcagtgatgagttccttttgtttgcgtgtgttttaaatatatgattttactttgtgaaaggatgcctcattgcctcttatttcaactgtataaagcccatgtgaattattcaatatattttactgaatatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGCG
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------------------------------------------------------------------------------------gtgagctattcttttgtctttctgctttgcttaatttat-tgcttcaaaatatcttccattctgatttgattttaaatcttaaatgacagGATTTCTATAGTGTACTTGGTGTCTCAAGAAATGCTAGTAAATCTGAAATCAAGAGCG
upper sequence: GLYMA05G31080.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0324g00040.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtttaaaat----gcactcttcagcagtgatgagttccttttgtttgcgt---gtgttttaaatatatgattttact--ttgtgaaaggatgcctcattgcctcttatttcaa---ctgtataaagcccatgtgaattattcaatatattttactgaatatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGCG
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gtgagtacaatgctttagtgtttctttgct-tcatgatggcaatggggctgtgcaaggtctctgaaatctgttactttgtcgctctcgttattgttccaaattaatttttgctctgcactctgcttgcaatactaatcaatggctgcataatccagattctggtactaacagtttttctcatgcagGATTTCTATTCTGTTCTTGGAGTGTCTAAAAATGCTAGCAAATCTGAAATTAAAAGCGMapped 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|17152831|gb|BM142764.1|BM142764EST: AAACTTTTAATCGTCGCAAGGGATCGAGGTTGATTGTTAGAGCTAATGCT GATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATT
genomic: AAACTTTTAATCGTCGCAAGGGATCGAGGTTGATTGTTAGAGCTAATGCTgtaagtttaa ... caacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATT
EST:
gi|26057478|gb|CA800392.1|CA800392EST: AAACTTTTAATCGTCGCAAGGGATCGAGGTTGATTGTTAGAGCTAATGCT GATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATT
genomic: AAACTTTTAATCGTCGCAAGGGATCGAGGTTGATTGTTAGAGCTAATGCTgtaagtttaa ... caacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatgtgaattattcaatatattttactgaatatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGCG
aattattcaatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttaaaatgcactcttcagcagtgatgagttccttttgtttgcgtgtgttttaaatatatgattttactttgtgaaaggatgcctcattgcctcttatttcaactgtataaagcccatgtgaattattcaatatattttactgaatatcctttatttgtcaacatgcagGATTATTATTCTGTCCTTGGGGTTTCAAGAAATGCTAGTAAATCTGAAATTAAGAGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA