Sequence
atgc intronic sequence ATGC exonic sequencegtatgctagctcattcatcttttgacagctataaatctcatattggtcttgaatcttgatgttgctgcttttgttgttgttcttaatattaactatgacacattcagttttttctcccttcagAACTACAGAAAATGAGTTCAGATCCAACCTATAATATAAACATGTCGGGTGATATAAAGCAAATGCTTAAGGAGCTTGGAACTGAGAAAGGGAAGGAAAC
Basic information
species | Glycine max |
transcript | GLYMA01G40170.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40170.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g10400.2 (Oryza sativa), 3'ss of exon 6
gtatgctagctcattcatcttttgacagctataaatctcatattggtcttgaatcttgatgttgctgcttt--tgttgttgttcttaatattaactatgacacatt--cagttttttctcccttcagAACTACAGAAAATGAGTTCAGATCCAACCTATAATATAAACATGTCGGGTGATATAAAGCAAATGCTTAAGGAGCTTGGAACTGAGAAAGGGAAGGAAAC
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-----------------------------------gttgattccggtccctc-tttcactcttacttctttcatattgctatttccta-gttaacttacatgctttatctgtatgactgttgctcagAGTTGCAACGAATGAAAAATGATCCAACCTACAACATAAATATTTCTGGTGATCTTAAGCAAATGATTAAGGAACTTGGAACTGAAAAGGGAAAGTTAGC
upper sequence: GLYMA01G40170.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G007486_T01 (Zea mays), 3'ss of exon 6
gtatgctagctcattcatcttttgacagctataaatctcatattggtcttgaatcttgatgttgctgcttttgttgttgttcttaatattaactatgacacattcagttttttctcccttcagAACTACAGAAAATGAGTTCAGATCCAACCTATAATATAAACATGTCGGGTGATATAAAGCAAATGCTTAAGGAGCTTGGAACTGAGAAAGGGAAGGAAAC
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--------------------gttaa--gttatgcttctctttccgtt-----accttttttccatttcagttgttcctgattaccttacatattctggca-atcgggttgttt-----tgcagAGTTGCAGCGGATGAAAGATGATCCAACCTATAACATAAATATTTCTGGTGATCTTAAGCAAATGATTAAGGAACTTGGGACAGAAAAAGGAAATGAAGC
upper sequence: GLYMA01G40170.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0129g00040.t01 (Vitis vinifera), 3'ss of exon 6
gtatgctagctcattcatcttttgacagctataaatctcatattggtcttga-atcttgatgttgctgcttttgttgttgttcttaatattaactatgacacattcagttttttctcccttcagAACTACAGAAAATGAGTTCAGATCCAACCTATAATATAAACATGTCGGGTGATATAAAGCAAATGCTTAAGGAGCTTGGAACTGAGAAAGGGAAGGAAAC
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----------------------------------gtgaagtattgtctataccacccttgtgggatcagaagtagaattgttctt--ctataattatgac---ttc---ttttctcttttccagAACTAAAAAAGATGGGTTTGGATCCAACCCATGGGATAAATGTGAAAGGGGATATGAAGCAAATGCTAGAGGAGCTTGGAACTGAGAAAGCAAGGCAAACMapped 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|208062424|gb|GD858080.1|GD858080EST: AAAATAGTTTGAAAGTTGATGATGAAG AACTACAGAAAATGAGTTCAGATCCAACCTATAACATAAACATGTCGGGTG
genomic: AAAATAGTTTGAAAGTTGATGATGAAGgtatgctagc ... ctcccttcagAACTACAGAAAATGAGTTCAGATCCAACCTATAATATAAACATGTCGGGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttgttgttcttaatattaactatgacacattcagttttttctcccttcagAACTACAGAAAATGAGTTCAGATCCAACCTATAATATAAACATGTCGGGTGATATAAAGCAAATGCTTAAGGAGCTTGGAACTGAGAAAGGGAAGGAAAC
tattaac putative branch site (score: 1)
cattcagttttttctc putative PPT
ttcttaatattaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctagctcattcatcttttgacagctataaatctcatattggtcttgaatcttgatgttgctgcttttgttgttgttcttaatattaactatgacacattcagttttttctcccttcagAACTACAGAAAATGAGTTCAGATCCAACCTATAATATAAACATGTCGGGTGATATAAAGCAAATGCTTAAGGAGCTTGGAACTGAGAAAGGGAAGGAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA