Sequence
atgc intronic sequence ATGC exonic sequencegtaaatatttattcagatttagattagattatttaatcagattttggaagtttgttttgacttacaatgtggttaatccctgtcactaacacaattttcagAACCAAACCCACATATGGGGCATCTGGCTTGGGCTGATGCATTTGTTGTCACAGCAGATTCAGTTAGCATGATAAGTGAAGCTTGCAGCACCGG
Basic information
species | Glycine max |
transcript | GLYMA13G39140.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G39140.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g33230.1 (Oryza sativa), 3'ss of exon 7
gtaaatatttattcagatttagat-tagattatttaatcagattttggaagtttgttttgacttaca-atgtggttaatccctgtcactaacacaattttcagAACCAAACCCACATATGGGGCATCTGGCTTGGGCTGATGCATTTGTTGTCACAGCAGATTCAGTTAGCATGATAAGTGAAGCTTGCAGCACCGG
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gtagatgaaatataacactaagttattcatgatgtaat-atatttattatgcatgttgttacatttgtaagttgtaacaagttgattttatt----tttgcagAACCTAACCCGCACATGGGGCATCTTGCATGGGCTGATGCTTTTGTTGTAACAGCTGATTCTATAAGTATGTTAAGTGAGGCTTGTAGCACAGG
upper sequence: GLYMA13G39140.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G22350.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaatatttattcagatttagattagattat--ttaatcagattttggaagtttgttttgacttacaatgtggttaatccctgtcactaacacaattttcagAACCAAACCCACATATGGGGCATCTGGCTTGGGCTGATGCATTTGTTGTCACAGCAGATTCAGTTAGCATGATAAGTGAAGCTTGCAGCACCGG
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----gtacctac---aatccagagcaaattttgcttgagctttgtgcacaagtacaatgcgaccacaaaagtttctaatgggtttttaaaattctaatt-cagAACCAAATCCTTACATGGGGCATCTAGCTTGGGGTGATGCTTTTGTGGTGACAGCAGATTCAGTCAGTCTGATAAGCGAAGCTTGTAGCACCGG
upper sequence: GLYMA13G39140.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0080g00830.t01 (Vitis vinifera), 3'ss of exon 7
gtaaatatttattcagatttagattagattatttaatcagattttggaagtttgttttgactt-acaatgtggttaatccctgtcactaacacaattttcagAACCAAACCCACATATGGGGCATCTGGCTTGGGCTGATGCATTTGTTGTCACAGCAGATTCAGTTAGCATGATAAGTGAAGCTTGCAGCACCGG
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gtaatc--ttagtcgatttgattctgaatgaatgaataaaat---ggaactaaaccatgatatgatcatctaatttata--tgttg-tgtgataatctatagAACCAAATCCACACATGGGACATCTAGCTTGGGCTGATGCTTTTGTTGTCACAGCAGATTCAGTGAGTATGATAAGTGAGGCTTGCAGCACAGG
upper sequence: GLYMA13G39140.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S82_141V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------gtaaata-tttattcagatttagattagattatttaatcagattttggaagtttg---ttttgacttacaatgtggttaatccct-gtcactaacacaattttcagAACCAAACCCACATATGGGGCATCTGGCTTGGGCTGATGCATTTGTTGTCACAGCAGATTCAGTTAGCATGATAAGTGAAGCTTGCAGCACCGG
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gtacattgtcataatattctctgacttcattgttttgttagtgatacttctcttaattctactaatatacaatttcctctttcatgtattattctatccaattttgttcccagagcttagattttcattttgtgggatgctaaagctcttggaattgattc--ttgtcagGTCCAAACCCGCACCTTGGACATCTCGCATGGGGGGATGCATTTGTTGTCACAGCTGATTCTGTTAGTATGTTGAGCGAAGCATGCAGCACAGGMapped 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|21887578|gb|BQ740791.1|BQ740791EST: AATAATCGGAAAGTTTATATTTGGGATGGGCAAG AACCAAACCCACATATGGGGCATCTGGCTTGGGCTGATGCATTTGTTGTCA
genomic: AATAATCGGAAAGTTTATATTTGGGATGGGCAAGgtaaatattt ... caattttcagAACCAAACCCACATATGGGGCATCTGGCTTGGGCTGATGCATTTGTTGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagtttgttttgacttacaatgtggttaatccctgtcactaacacaattttcagAACCAAACCCACATATGGGGCATCTGGCTTGGGCTGATGCATTTGTTGTCACAGCAGATTCAGTTAGCATGATAAGTGAAGCTTGCAGCACCGG
cactaac putative branch site (score: 1)
ttttc putative PPT
acaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatatttattcagatttagattagattatttaatcagattttggaagtttgttttgacttacaatgtggttaatccctgtcactaacacaattttcagAACCAAACCCACATATGGGGCATCTGGCTTGGGCTGATGCATTTGTTGTCACAGCAGATTCAGTTAGCATGATAAGTGAAGCTTGCAGCACCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC