Sequence
atgc intronic sequence ATGC exonic sequence...attaaaaaatatgcattctgagatttttaaaacatgatatattggtggtggaattagcagcagagagtttttctgatatgctacattcttaatctggtagGCAAGTAATTTACGAGTGATGCTTTTGGGAATGGTTGATGATCCACGTGTTGTGCTCATCAAGCTTGCAGATCGTCTTCACAACATGAGAACAAT
Basic information
species | Glycine max |
transcript | GLYMA01G43930.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G43930.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G106931_T01 (Zea mays), 3'ss of exon 4
attaaaaaatatgcattctgagatttttaaaacatgatatattggtg-gtggaattagcagcagagagtttttctgatatgctacattcttaatctggtagGCAAGTAATTTACGAGTGATGCTTTTGGGAATGGTTGATGATCCACGTGTTGTGCTCATCAAGCTTGCAGATCGTCTTCACAACATGAGAACAAT
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atatcagcatcttc-tgacaaaactgttgtgagatgccagaaaagtatataaaactgctttctgaaagccgtggtttgattatcctcttgttgtcagtcagGCAAATAATCTACGTGTTATGTTATTGGGGATGGTTGATGATCCTCGTGTGGTGCTCATCAAGCTGGCAGATCGCTTGCACAATATGCGGACAAT
upper sequence: GLYMA01G43930.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0039g02260.t01 (Vitis vinifera), 3'ss of exon 5
attaaaaaatatgcattctgagatttttaaaacatgatatattggtggtggaattagcagcagagagtttttctgatatgctacattcttaatctggta-----gGCAAGTAATTTACGAGTGATGCTTTTGGGAATGGTTGATGATCCACGTGTTGTGCTCATCAAGCTTGCAGATCGTCTTCACAACATGAGAACAAT
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gtatgatttcatgagttttt-gcctctgaagacaag-catat--gagaaccagttttcagctgc-attagttttattatgtcacaatttcaatgtgatatttcagGCAAACAATTTGCGAGTCATGCTTTTGGGCATGGTTGATGATCCGCGTGTTGTACTCATCAAGCTTGCAGATCGTCTTCATAACATGAGAACAAT
upper sequence: GLYMA01G43930.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S15_331V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------attaaaaaatatgcattctgagatttttaaaacatg----atatattggtggtggaat-tagcagcagagagtttttctgatatgctacattctta-----at----ctggt---------agGCAAGTAATTTACGAGTGATGCTTTTGGGAATGGTTGATGATCCACGTGTTGTGCTCATCAAGCTTGCAGATCGTCTTCACAACATGAGAACAAT
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gtaggtttaatacagaggactcaatcgagcgtctgatacgatgtcttgtaatttggaga-ggatattttggaaatttcgaggaatgttgaatatacgcacactggtctcttgaagcgacgtagtttattgattctgtggacactgatgcgcatggcactggtgcaaattccagGTAGATGATTTGCGTATGATGTTATTGGGTATGGTCAATGATCCACGGGTGGTGTTGATCAAACTTGCTGATCGTCTTCACAACATGCGGACAATMapped 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|11413043|gb|BF425063.1|BF425063EST: GCAGACATCGGAGGGTAAGTGTAAACCAGGGTGTCCTTGGCCAAGAAGAG GCAAGTAATTTACGAGTGATGCTTTTGGGAATGGTTGATGATCCACGTGTT
genomic: GCAGACATCGGAGGGTAAGTGTAAACCAGGGTGTCCTTGGCCAAGAAGAGgtacataatt ... aatctggtagGCAAGTAATTTACGAGTGATGCTTTTGGGAATGGTTGATGATCCACGTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtggaattagcagcagagagtttttctgatatgctacattcttaatctggtagGCAAGTAATTTACGAGTGATGCTTTTGGGAATGGTTGATGATCCACGTGTTGTGCTCATCAAGCTTGCAGATCGTCTTCACAACATGAGAACAAT
tcttaat putative branch site (score: 3)
attcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attaaaaaatatgcattctgagatttttaaaacatgatatattggtggtggaattagcagcagagagtttttctgatatgctacattcttaatctggtagGCAAGTAATTTACGAGTGATGCTTTTGGGAATGGTTGATGATCCACGTGTTGTGCTCATCAAGCTTGCAGATCGTCTTCACAACATGAGAACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- -aaaaaat
- - - - - - gcattct
- - - - - - - - - - - - - - - - catgata
- - - - - - - - - - - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -agcagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctaca