Sequence
atgc intronic sequence ATGC exonic sequence...ttatattgcaaaacagtatctagacatagttatactcaaatatattatgtagctagccttaatgttttgtgtaatatattttctgtttctcctctggcagCTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC
Basic information
species | Glycine max |
transcript | GLYMA12G34400.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G34400.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g46930.1 (Oryza sativa), 3'ss of exon 2
ttatattgcaaaacagtatctagacatagttatactcaaatatattatgtagctagccttaatgttttgtgtaatatattttctgtttctcctctggcagCTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC
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-----------------------gtaagtttcaattcttttttggtctgcagcttgctatttactcaaatgtctgaaatttccc-tttttccaatg-cagCTTAAGCGATGGGAGAGGAAGAAGTGTAAACCAAACAGTCTTCCTGTCCTGCACAAGATGCATGTTAGGATTGGCGATACAGTACAAGTCATTGCAGGCC
upper sequence: GLYMA12G34400.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G463913_T01 (Zea mays), 3'ss of exon 2
ttatattgcaaaacagtatctagacatagttatactcaaatatattatgtagctagccttaatgttttgtgtaatatattttctgtttctcctctggcagCTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC
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--gtgagtaaaaaaaatctttagtccaa---atatttga-taccttttttatccaa---taatgtgaaatgtcctaaaacttcactttccact---gcagCTTAAGAGATGGGAGCGAAAGAAGTGTAAACCAAACAGTCTTCCTGTGCTGCACAAGATGCATGTTAGGATCGGGGACACGGTACAGGTTATTGCAGGCC
upper sequence: GLYMA12G34400.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G54600.2 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------------ttatattgcaaaacagtatctagacat----agttatactcaaatatattatgtagctagccttaatgttttg----tgtaatatattttctgt-ttctcctctggcagCTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC
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gttagtccacagatccattacattaacattctgcattattcgttaatatactagctttgaaaccacaataattctttagattttgtacacatcaaaagcaaaaaggaaaactgttg-atagattcttttgaaacaatgagattggaagatgatttatgtgttttgcgttttcagCTCAAGCGTTGGGAACGAAAAGAATGCAAACCAAACAGTCTTCCGATTCTCCACAAAATGCATGTCAAGTTTGGAGATACAGTCAAAGTAATATCTGGAC
upper sequence: GLYMA12G34400.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0014g04970.t01 (Vitis vinifera), 3'ss of exon 2
ttatattgcaaaacagtatctagacatagttatactcaaatatatt--atgtagctagccttaatgtt-ttgtgtaatatattttctgtttctcctctggcagCTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC
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--ctgtctgagcaacgcaaaaatccatgagt-tacttgatgatcatgaacatggcttctcttaaaaataccaagtggttttactttgtctttacctcatgcagCTTAAGCGATGGGAGCGGAAGGAATGCAAACCCAACAGCCTTCCGGTGCTACATAAAATGCATGTTAAGGTGGGAGATACAGTGAAAATAATATCTGGTAMapped 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|298166988|gb|HO010427.1|HO010427EST: GGTAAGTCAACAGAGAAGCAATGTCCCATTGTAATGAGG CTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTG
genomic: GGTAAGTCAACAGAGAAGCAATGTCCCATTGTAATGAGGgttagtatca ... cctctggcagCTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtagctagccttaatgttttgtgtaatatattttctgtttctcctctggcagCTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC
ccttaat putative branch site (score: 4)
tatattttctgtttct putative PPT
ttaatgttttgtgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatattgcaaaacagtatctagacatagttatactcaaatatattatgtagctagccttaatgttttgtgtaatatattttctgtttctcctctggcagCTTAAACGATGGGAGCGGAAGGAGTGTAAACCAAACAGTCTTCCTATCTTGCACAAAATGCATGTTAAACTTGGAGATACGGTGCAAGTCATATCTGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT