Sequence
atgc intronic sequence ATGC exonic sequence...attttccctgtttgataaagaagtgtacttctagagtagctagctattcatggaaagaactttaattctgaacaagtgttctttgtgtctttcctcacagTTGATGAACGCTGTGATATGGAACTTGATGAGACAGATCCGACTATCTGGCTAAAGTTGGAATCTGCGATTGAAGAATATATACAAAAGAATCATCACGC
Basic information
species | Glycine max |
transcript | GLYMA07G38890.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G426556_T01 (Zea mays), 3'ss of exon 11
-------------------------------------------------------------attttccctgtt-tgataaagaagtgtacttc--tagagtagctagctattcatggaaagaactttaat-tctgaacaagtgttctttgtgtctttcctcacagTTGATGAACGCTGTGATATGGAACTTGATGAGACAGATCCGACTATCTGGCTAAAGTTGGAATCTGCGATTGAAGAATATATACAAAAGAATCATCACGC
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gtaaatcaactcaaaggaaactcttagcatttgctagaagagaaactattaatgtgctgggatctgtagcatcataaccataatttgttgtgcactacttttgatatgtttcaacctaattaacctgcatattcaaatgagtgaactctcaatgttg----gcagTGGATGAACGGTGTGGTATGGAGTTAGATGAAACTGATCCTACTATCTGGCTGAAGTTGGAAGCTGCAACTGATGAGTACATTCAGAAGAACTTTCTGTC
upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 13
----------------------------------attttccctgtttgata---aagaag---tgtacttctagagtagctagctattcatg--gaaagaactttaattctgaac--aagtgttctttgtgtctttcctca----cagTTGATGAACGCTGTGATATGGAACTTGATGAGACAGATCCGACTATCTGGCTAAAGTTGGAATCTGCGATTGAAGAATATATACAAAAGAATCATCACGC
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gtaacaaacagcattttacaacatgcaagaacactcttatcctgttgaacacctatgaaaccttgaatttcttatccatgccgatttccataatgcatgtgttttgacgtagaatctagttaatctttacatatctgggtatatgcagTTGACGATCGCTGTGGAATGGAGTTGGATGAGACTGATCCAGCGATCTGGCTAAAATTGGAAGCTGCGATTGAAGAATTCATACAAAGCAATCCCCAAGT
upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv10s0116g00830.t01 (Vitis vinifera), 3'ss of exon 13
-----attttc-cctgtttgataaagaagtgtacttctagagtagctagctattcatggaaagaactttaattctgaacaagtgttctttgtgtctttcctcacagTTGATGAACGCTGTGATATGGAACTTGATGAGACAGATCCGACTATCTGGCTAAAGTTGGAATCTGCGATTGAAGAATATATACAAAAGAATCATCACGC
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ttctgattctaaccttcttaatatagaa---tactatcttaattagtagcttctgatgaaagaaatttgaaatctg--taaacattttatat-tttcttttaacagTTGATGAACGGTGTGATATGGAGCTGGATGAGACTGATCCTGCAGTCTGGCTAAAATTGGAAGCTGCAACTGAGGAGTACATCCAGAACAACTCCCAGGCMapped 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|13311431|gb|BG405082.1|BG405082EST: TACATTGCTACCCATGCTTCCTGAGATACAATATTTTCGTTTCAATCCAG TTGATGAACGCTGTGATATGGAACTTGATGAGACAGATCCAACTAACTGGC
genomic: TACATTGCTACCCATGCTTCCTGAGATACAATATTTTCGTTTCAATCCAGgtatttgata ... ttcctcacagTTGATGAACGCTGTGATATGGAACTTGATGAGACAGATCCGACTATCTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcatggaaagaactttaattctgaacaagtgttctttgtgtctttcctcacagTTGATGAACGCTGTGATATGGAACTTGATGAGACAGATCCGACTATCTGGCTAAAGTTGGAATCTGCGATTGAAGAATATATACAAAAGAATCATCACGC
ctttaat putative branch site (score: 4)
ttctttgtgtctttcc putative PPT
aaagaactttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttccctgtttgataaagaagtgtacttctagagtagctagctattcatggaaagaactttaattctgaacaagtgttctttgtgtctttcctcacagTTGATGAACGCTGTGATATGGAACTTGATGAGACAGATCCGACTATCTGGCTAAAGTTGGAATCTGCGATTGAAGAATATATACAAAAGAATCATCACGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- -ttccctg
- - - - - - - - - - -agtgtac
- - - - - - - - - - - - - - - - - - - - - - - - catggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgaac