Sequence
atgc intronic sequence ATGC exonic sequence...ttctgctgaagaagaaatgtttaagggtgaaaagaaacaaaggctcaattgagtcaacgacattgttaacaattttcttttgttgcttttgtctatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
Basic information
species | Glycine max |
transcript | GLYMA13G34560.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 3
--ttctgctgaagaagaaatgtttaagggtgaaaagaaacaaagg---ctca--attgagtcaacgacattgttaa-caattttcttttgttgc------ttttgtctatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
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gtacttgttgcaaacattatgttcatttacaaaatgctttgcattattttcagcatgaggtcagaaagatccataatccattcttatgcttcacctgacatcctattattttagATCCAAGCTGCCTTTAGAACCGATGAGATCCGAAGAACACAGCCCACTCCCCAAGATGAAATGCGTGCTGGCATGAGCTACTTCCATGAAACAATATGGA
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 3
-ttctgctgaagaagaaatgtttaagggtgaaaagaaacaaaggctcaattgagtcaacgacattgttaacaattttcttttgt-----tgcttttgtctatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
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gtacttctttcaatctaattttattacctaaaattctttgaagcttgagaccaaagagattaattcttaatttcttacctgaatacctctctctttctttttcaagATCCAAGCTGCCTTTAGAACTGATGAGATCCGAAGAACACAGCCCACTCCCCAAGATGAAATGCGTGCTGGTATGAGCTACTTCCACGAAACAATTTGGA
upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 3
ttctgctgaagaagaaatgtttaagggtgaaaagaaacaaaggctcaattgagtcaacgacattgttaacaattttcttttgttgcttttgtctatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
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aattgctctatttgagttacaaatgaagattgttgtttggaggcttgcccgaaatacgaccgtttttctgaattaccattttctgttatttttcctgcagATTCAAGCAGCATTTCGCACAGATGAGATCCGGAGGACCCCTCCTACTCCACAAGATGAGATGAGGGCAGGAATGAGTTATTTCCATGAAACAATCTGGAMapped 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|18730061|gb|BM525657.1|BM525657EST: ACATTACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAG ATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCA
genomic: ACATCACTCCTGATGATAAGCAGGAGCTTGATGAGGCTCTACAAAGGGAGgtgagtgtca ... gtctatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caattgagtcaacgacattgttaacaattttcttttgttgcttttgtctatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
tgttaac putative branch site (score: 2)
ttttcttttgttgctt putative PPT
ttaacaattttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctgctgaagaagaaatgtttaagggtgaaaagaaacaaaggctcaattgagtcaacgacattgttaacaattttcttttgttgcttttgtctatgtagATTCAAGCTGCCTTCCGTACAGATGAAATCAGGAGGACCCCTCCAACACCACAAGATGAGATGAGAGCAGGGATGAGCTACTTCCATGAAACAATTTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- ctgctga
- - - - -agaagaaa
- - - - - - - - - - - - - - - aaagaaa