Sequence
atgc intronic sequence ATGC exonic sequencegtttttatttgttttgttgctatactttatctacagtttatgttgttagtgataaaaatgtatgattagttatctgtgttttagatctcttttaatatactagattacatattctgatttgatttgatgttaatgcaacacagGAGAAGGCTGGAAAAGCGTATATATATCCCTCTTCCAAATTTTGAGAGTCGTAAAGAGCTGATCCGAATCAATTTGAAGACTGTTGAG
Basic information
species | Glycine max |
transcript | GLYMA07G03820.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 5
gtttttatttgttttgttgctatactttatctacagtttatgttgttagtgataaaaatgtatgattagttatctgtgttttagatctcttttaatatactagattacatattctgatttgatttgatgttaatgcaacacagGAGAAGGCTGGAAAAGCGTATATATATCCCTCTTCCAAATTTTGAGAGTCGTAAAGAGCTGATCCGAATCAATTTGAAGACTGTTGAG
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------------------------------------gctatgttttgggacagaggaa---gcactt--ttgttcttacttttaatcttccgaacggtgtccgtatacaacctctaactct-tacattcttgattca-ctcagACGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAAATTTTGAAAGCAGAAAGGCACTCATCAATATTAACCTTAAAACTGTTGAG
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttttatttgttttgttgctatactttatctacagtttatgttgttagtgataaaaatgtatgattagttatctgtgt-tttagatctcttttaatatact-agattacatattctgatttgatttgatgttaatgcaacacagGAGAAGGCTGGAAAAGCGTATATATATCCCTCTTCCAAATTTTGAGAGTCGTAAAGAGCTGATCCGAATCAATTTGAAGACTGTTGAG
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---------------------------------------------------gtttaaatattctttgagttaatgccgtctttagacttgctctaatataatgaaattgctgattctg----gagctcacgttggtgca-----gGAGGAGGTTGGAAAAACGTATATATATCCCACTTCCAGATTTTGAAAGTCGTAAGGCTCTTATCAATATCAATCTGAGAACAGTTGAG
upper sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 5
gtttttatttgttttgttgctatactttatctacagttta-tgttgttagtgataaaaatgtatgattagtt-atctgtgttttagatctcttttaatata---ctagattacatattctgatttgatttgatgttaatgcaacacagGAGAAGGCTGGAAAAGCGTATATATATCCCTCTTCCAAATTTTGAGAGTCGTAAAGAGCTGATCCGAATCAATTTGAAGACTGTTGAG
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-------gttgtatc-tcattattttttttttaaaattaaatatttttttttttgaatttttatcattctttgaattgttaagtagatttaatctaggatttttctgttctaagcagtcc-atttgaaa-gatttttatgtaatgcagGAGGAGGCTGGAAAAGCGTATATACATCCCTCTCCCAAATTTTGAGAGTCGCAAGGAGCTTATACGGATCAATTTGAAAACTGTGGAGMapped 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|11274568|gb|BF324910.1|BF324910EST: ATGGTTTTGGCCGCTACTAACTTCCCTTGGGATATAGATGAGGCACTAAG GAGAAGGCTGGAAAAGCGTATATATATCCCTCTTCCAAATTTTGAGAGTCG
genomic: ATGGTTTTGGCAGCTACTAACTTCCCTTGGGATATTGATGAGGCACTAAGgtttttattt ... tgcaacacagGAGAAGGCTGGAAAAGCGTATATATATCCCTCTTCCAAATTTTGAGAGTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttaatatactagattacatattctgatttgatttgatgttaatgcaacacagGAGAAGGCTGGAAAAGCGTATATATATCCCTCTTCCAAATTTTGAGAGTCGTAAAGAGCTGATCCGAATCAATTTGAAGACTGTTGAG
tgttaat putative branch site (score: 3)
aatatactagatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttatttgttttgttgctatactttatctacagtttatgttgttagtgataaaaatgtatgattagttatctgtgttttagatctcttttaatatactagattacatattctgatttgatttgatgttaatgcaacacagGAGAAGGCTGGAAAAGCGTATATATATCCCTCTTCCAAATTTTGAGAGTCGTAAAGAGCTGATCCGAATCAATTTGAAGACTGTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA