Sequence
atgc intronic sequence ATGC exonic sequence...ctggtagacacccaagagtaatgaattattatgtatgttcatagatccactccacttcacatgacacatgtaattcaggtttctgacaactgttcttcagATTTTTCGGTTTTGTAGATCTAAATGCCACAAAAACTTTAAAATGAAGAGGAACCCTCGGAAAGTAAAATGGACAAAGGCATATAGACGAGTGCATGGAA
Basic information
species | Glycine max |
transcript | GLYMA12G09090.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G09090.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g33050.2 (Oryza sativa), 3'ss of exon 1
ctggtagacacccaagagtaatgaattattatgtatgttcatagatccactccacttcacatgacacatgtaattcaggt------ttctgacaactgttctt--------cagATTTTTCGGTTTTGTAGATCTAAATGCCACAAAAACTTTAAAATGAAGAGGAACCCTCGGAAAGTAAAATGGACAAAGGCATATAGACGAGTGCATGGAA
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--------------ggaatgtaacattttttttcccttgcagatcttcccttgcattcctataacaagctggattttgtcggtatgctgtaacaacattttttttcccttgcagATCTTCCGCTTTTGCCGGTCAAAATGCCATAAAAATTTTAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCATACAGATGCTTGCATGGGA
upper sequence: GLYMA12G09090.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
ctggtagacacccaagagtaatgaattattatgtatgt-tcatagatccactccacttcacatgacacatgtaattcaggtttctgacaactgttctt----cagATTTTTCGGTTTTGTAGATCTAAATGCCACAAAAACTTTAAAATGAAGAGGAACCCTCGGAAAGTAAAATGGACAAAGGCATATAGACGAGTGCATGGAA
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ttgattggcacttc----ttatatattattgtttgctcatcaaaaaaatgtttta-tacccccaactgtagtgccactacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
upper sequence: GLYMA12G09090.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0061g01330.t01 (Vitis vinifera), 3'ss of exon 1
-------------------ctggtagacacccaagagtaatgaatt---attatgtatg--ttcatagatccactccac--ttcacatgacacatgtaattcaggtttctgac---aactgttcttcagATTTTTCGGTTTTGTAGATCTAAATGCCACAAAAACTTTAAAATGAAGAGGAACCCTCGGAAAGTAAAATGGACAAAGGCATATAGACGAGTGCATGGAA
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attagctggtattggagtattgctctgctctcccatgttatcaaatcaagttaggaatgcattaatcactgcttgcaatcgtttctttattgctcatagcTCAAGTTCCTGATGGTAATCAATCTGCAGATTTTTCGGTTCTGTCGATCCAAATGCCACAAGAACTTCAAGATGAAGCGGAATCCTCGTAAAGTAAAATG-----------------------------Mapped 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|298190182|gb|HO032303.1|HO032303EST: CTACCATATACCCTGGACATGGAATCCAGTTTGTTCGTAATGATGCAAAG ATTTTTCGGTTTTGTAGATCTAAATGCCACAATAACTTTAAAATGAAGAGG
genomic: CTACCATATACCCTGGACATGGAATCCAGTTTGTTCGTAATGATGCAAAGgtaagctcat ... tgttcttcagATTTTTCGGTTTTGTAGATCTAAATGCCACAAAAACTTTAAAATGAAGAGG
EST:
gi|6070529|gb|AW099916.1|AW099916EST: CTACCATATACCCTGGACATGGAATCCAGTTTGTTCGTAATGATGCAAAG ATTTTTCGGTTTTGTAGATCTTAATGCCACAAAAACTTTAAAATGAAGAGG
genomic: CTACCATATACCCTGGACATGGAATCCAGTTTGTTCGTAATGATGCAAAGgtaagctcat ... tgttcttcagATTTTTCGGTTTTGTAGATCTAAATGCCACAAAAACTTTAAAATGAAGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccactccacttcacatgacacatgtaattcaggtttctgacaactgttcttcagATTTTTCGGTTTTGTAGATCTAAATGCCACAAAAACTTTAAAATGAAGAGGAACCCTCGGAAAGTAAAATGGACAAAGGCATATAGACGAGTGCATGGAA
ttctgac putative branch site (score: 2)
ctgttcttc putative PPT
atgtaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctggtagacacccaagagtaatgaattattatgtatgttcatagatccactccacttcacatgacacatgtaattcaggtttctgacaactgttcttcagATTTTTCGGTTTTGTAGATCTAAATGCCACAAAAACTTTAAAATGAAGAGGAACCCTCGGAAAGTAAAATGGACAAAGGCATATAGACGAGTGCATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - gacaccc
- - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgac