Sequence
atgc intronic sequence ATGC exonic sequence...gtttgttctttaattagtaacaacaattgaaccttgtttttctgtttttcaatgactgctgtaatgtggacaattatgccttatgttgttgtgggtgtagGAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTTAAGTCCGTTC
Basic information
species | Glycine max |
transcript | GLYMA12G02010.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G02010.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g59630.1 (Oryza sativa), 3'ss of exon 2
gtttgttctttaattagtaacaacaattgaaccttgtttttctgtttttcaatgactgctgtaatgtggacaattatgcc-ttatgttgttgtgggtgt-agGAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTTAAGTCCGTTC
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gtggctaggtttatttacagaaggatattgtcatgaaatttct--tcacccaagtttatttgcaagaggacagtattgatattgttgttttgttggtgttagGAAGCTTTGAAATGGGTTACTGATCAACCTGCTTGGCAACGTTCAGAAGGCAGAGATCATGTAATTCCCGTTCATCACCCATGGTCGTTTAAGTCAGTTC
upper sequence: GLYMA12G02010.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G139691_T01 (Zea mays), 3'ss of exon 2
gtttgttctttaa----ttagtaacaacaattgaaccttgtttttctgtttttcaatgactgctgtaatgtggacaattatgccttatgttgttgtgggtgtagGAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTTAAGTCCGTTC
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----atcatttaagatctttatctctgtgtatggaaattactttattgttattcacttcaatttattccaagaggaacttatcatcattacatcttgatgttagGAAGCTTTGAAATGGGTCACAGATCAGCCTGCTTGGCAACGTTCAGAAGGCAGGGATCATGTCATTCCTGTTCATCATCCATGGTCATTTAAGTCAGTCC
upper sequence: GLYMA12G02010.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G16890.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgttctttaattagtaacaacaattga-accttgtttttctgtttttcaatgactgctgtaatgtggacaattatgccttatgttgttgtggg-tgtagGAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTTAAGTCCGTTC
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-attcaggttaagcctgcctcaatgggagatgtattagttgaaaaacatgagatgccagattttac-tggtaatatattttttaactctttttaaactgtagGAAGCTTTGAAGTGGGTCACTGATCAGCCTGCTTGGAAGAGGTCCGAGGGAAGGGATCACATATTTCCTATTCATCATCCTTGGTCCTTCAAGTCTGTCC
upper sequence: GLYMA12G02010.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0014g00560.t01 (Vitis vinifera), 3'ss of exon 2
gtttgttctttaattagtaacaacaattgaaccttgtttttctgtttttcaatgactgctgtaatgtggacaattatg--ccttatgttg---ttgtgggtgtagGAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTTAAGTCCGTTC
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----atcacctatggggtaatcataaattagt-ttgtttctgagaatataattgtaatgtaaagtctagcttattctaaacatcaaatttatcttgtggatgtagGAAGCTTTGAAGTGGGTGACTGATCAACCTGCATGGAAACGGTCTGAAGGGAGGGACCACATACTTCCAGTTCATCATCCATGGTCTTTCAAGACTGTTCMapped 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|10232714|gb|BE801602.1|BE801602EST: CTATCAGCTTCTTCCTCATGGAAAAACAACAATGCAAGGCCCTTTATAGG GAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGC
genomic: CTATCAGCTTCTTCCTCATGGAAAAACAACAATGCAAGGCCCTTTATAGGgtgtgagtgc ... gtgggtgtagGAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcaatgactgctgtaatgtggacaattatgccttatgttgttgtgggtgtagGAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTTAAGTCCGTTC
acaattat 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
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gtttgttctttaattagtaacaacaattgaaccttgtttttctgtttttcaatgactgctgtaatgtggacaattatgccttatgttgttgtgggtgtagGAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTTAAGTCCGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA