Sequence
atgc intronic sequence ATGC exonic sequencegttcatttatctggccattttggtgtgtttttttgctagtgactgcagagtttctgagaggacattcatgtctttttttttagattttaataccttagaattggaacttctgtctctgaagcatagGTTTATCAAGCTAGGCTTCGCAAAACAGGACAGGTTGTTGCTGTTAAAGTGCAAAGACCAGGAGTTCAAGCAGCAATTTCCCTTGACATATTAATCTTGC
Basic information
species | Glycine max |
transcript | GLYMA16G27500.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g54790.1 (Oryza sativa), 3'ss of exon 4
gttcatttatctggccattttggtgtgtttttttgctagtgactgcagagtttctgagaggacattcatgtctttttttttagattttaataccttagaattggaacttctgtctctgaagcatagGTTTATCAAGCTAGGCTTCGCAA-AACAGGACAGGTTGTTGCTGTTAAAGTGCAAAGACCAGGAGTTCAAGCAGCAATTTCCCTTGACATATTAATCTTGC
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-------------------atgttgaacaattggtgaaatgacagtgatactctgtatagtgcattgtcagatattttcatc--tctggacgatataacatttcatattctactattg-----tagGTTTATCAGGCCAGGCTTCGTTCCAACAGGA-AGGTTGTTGCTGTCAAAGTACAAAGACCTGGAGTTCAAGCAGCAATTTCCTTGGATATCTACATCTTGA
upper sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G305007_T02 (Zea mays), 3'ss of exon 3
gttcatttatctggccattttggtgtgtttttttgctagtgactgcagagtttctgaga-ggacattcatgtctttttttttagattttaataccttagaattggaacttctgtctctgaagcatagGTTTATCAAGCTAGGCTTCGCAAAACAGGACAGGTTGTTGCTGTTAAAGTGCAAAGACCAGGAGTTCAAGCAGCAATTTCCCTTGACATATTAATCTTGC
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-------------------atgataaattcaaatattagtcaattcacacttcctagcatggacaaccgtggcatttcatctccagtgatacaatgttcaatt----tttcttacttt----tgtagGTTTACCAGGCTAGGCTCCGCTCCAGTGGGAAGATTGTTGCTGTCAAAGTACAAAGACCTGGAGTTCAAGCAGCAATTTCATTAGACATATATATCTTGA
upper sequence: GLYMA16G27500.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g01620.t01 (Vitis vinifera), 3'ss of exon 4
gttcatttatctggccattttggtgtgtttttt-tgctagtgactgcagagtttctgagaggacattcatgtctttttttttagattttaat--accttagaattggaacttctgtctctgaagcatagGTTTATCAAGCTAGGCTTCGCAAAACAGGACAGGTTGTTGCTGTTAAAGTGCAAAGACCAGGAGTTCAAGCAGCAATTTCCCTTGACATATTAATCTTGC
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----------------------gtttactttcaattatacttggtgcttgtcaccttgggatatgttgcctatttttcttcaagattgaaactcatcacagaccccccataacaaaaaattttatttagGTTTATCAAGCTAGGCTTTGTCCTAGTGGTCAGGTTGTTGCTGTCAAAGTGCAGAGGCCTGGGGTTCAAGCTGCTATTTCCTTGGACATATTAATCTTGCMapped 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|15662324|gb|BI699695.1|BI699695EST: TTTTCTCAGAGATTTCACCTGAGCCAGTAGCTGCTGCATCCCTTGGGCAG GTTTATCAAGCTAGGCTTCGCAAAACAGGACAGGTTGTTGCTGTTAAAGTG
genomic: TTTTCTCAGAGATTTCACCTGAGCCAGTAGCTGCTGCATCCCTTGGGCAGgttcatttat ... tgaagcatagGTTTATCAAGCTAGGCTTCGCAAAACAGGACAGGTTGTTGCTGTTAAAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttttttagattttaataccttagaattggaacttctgtctctgaagcatagGTTTATCAAGCTAGGCTTCGCAAAACAGGACAGGTTGTTGCTGTTAAAGTGCAAAGACCAGGAGTTCAAGCAGCAATTTCCCTTGACATATTAATCTTGC
ttttaat putative branch site (score: 3)
cttctgtctct putative PPT
tttttagattttaata 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
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gttcatttatctggccattttggtgtgtttttttgctagtgactgcagagtttctgagaggacattcatgtctttttttttagattttaataccttagaattggaacttctgtctctgaagcatagGTTTATCAAGCTAGGCTTCGCAAAACAGGACAGGTTGTTGCTGTTAAAGTGCAAAGACCAGGAGTTCAAGCAGCAATTTCCCTTGACATATTAATCTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG