Sequence
atgc intronic sequence ATGC exonic sequence...attttcccctatagattgcaacttctttctcattttcatactaagtctccatgtttaaaaattgatttaagtttgacaaattttccttgcttttaaaaagCTCATAGGCTCACCTGATGACACTAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATATGTGAGACAGCTTCCACAATATCCAAGGCAACAATTTG
Basic information
species | Glycine max |
transcript | GLYMA09G39190.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 4
attttcccctatagattgcaacttctttctcattttcatactaagtctccatgtttaaaaattgatttaagtttgacaa-attttccttgcttt----taaaaagCTCATAGGCTCACCTGATGACACTAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATATGTGAGACAGCTTCCACAATATCCAAGGCAACAATTTG
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-----ctgaaactgacttgcactccttttctactgaatgggttatctcctacagttttgatctattctgtttataactttatttttcactctttgatccaaaaagTTAATAGGCTCACCTGATGACTCGAGCCTTGGGTTTCTTCGAAGCGACAACGCCCGCAGATATGTGAGGTCGCTTCCTCAATACCCCAAGCAACAATTCC
upper sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
attttcccctatagat-tgcaacttc---tttctcattttcatactaagtctccatgtttaaaaattgatttaagtttgacaaattttccttgcttttaaaaagCTCATAGGCTCACCTGATGACACTAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATATGTGAGACAGCTTCCACAATATCCAAGGCAACAATTTG
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-ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctac-tataatctgggcattaattttaatgagttttttct--cttccaaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
upper sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 4
attttcccctatagattgcaacttctttctcattttcatactaagtctccatgtttaaaaattgatttaagtttgaca--------aattttccttgcttttaaaaagCTCATAGGCTCACCTGATGACACTAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATATGTGAGACAGCTTCCACAATATCCAAGGCAACAATTTG
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-------agaactggtggtggcattgttggaaggtgaagtttctgtttctct-tatagcatttggttcaattctgatacttgctttgtttttctttttccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAATGCCCGAAGATATGTTAGGCAGCTACCACAATACCCGAGACAACAATTTCMapped 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|31466355|gb|CD408383.1|CD408383EST: CCCTATTTCTGGGGAAAGATTATGTTCATCAGCTCAGGCTGATTACGGAG CTCATAGGCTCACCTGATGACACTAGCCTTGGATTTCTACGAAGTGATAAT
genomic: CCCTATTTCTGGGGAAAGATTATGTTCATCAGCTCAGGCTGATTACGGAGgtattagcta ... ttttaaaaagCTCATAGGCTCACCTGATGACACTAGCCTTGGATTTCTACGAAGTGATAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctccatgtttaaaaattgatttaagtttgacaaattttccttgcttttaaaaagCTCATAGGCTCACCTGATGACACTAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATATGTGAGACAGCTTCCACAATATCCAAGGCAACAATTTG
gtttgac putative branch site (score: 4)
ttttccttgctttt putative PPT
atgtttaaaaattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttcccctatagattgcaacttctttctcattttcatactaagtctccatgtttaaaaattgatttaagtttgacaaattttccttgcttttaaaaagCTCATAGGCTCACCTGATGACACTAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATATGTGAGACAGCTTCCACAATATCCAAGGCAACAATTTG
- tttcccc
- - - - - - - - tgcaact
- - - - - - - - - - - - - - - - - - - - - - - - ccatgtt