Sequence
atgc intronic sequence ATGC exonic sequence...caaaaccagcttcttagaaaggtccttttaattttttagggtgatatgatggtaagttttgaaattttatgatcttctaagctttcgccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAAAACTCTGGCAAG
Basic information
species | Glycine max |
transcript | GLYMA17G30770.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G30770.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g48160.3 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------caaaaccagcttcttagaaaggtccttttaattttttagggtgatatgatggtaagttttgaaattttatgatcttctaagctttcgccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAAAACTCTGGCAAG
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gtaccaagcattccatttcaggtttttttcagttgggcaatgctgtttctgggcttccctgttttctgaactttctgttgctatatgcttttctgattacaccaaaacagctgccaattgactgctatttgtatttcttgtctatatgccagAAACCGGAGTCATGGAGGCTTGCTTGTCAGACTATTGTTGGAAACAAAGAAAATTCCGGCAAG
upper sequence: GLYMA17G30770.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G470653_T01 (Zea mays), 3'ss of exon 4
--caaaaccagcttcttagaaaggtccttttaattttttagggtgatatgatggtaagttttgaaattttatgatcttctaagctttcgccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAAAACTCTGGCAAG
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gtaggcattggacact--ggacagcgcgtacagttcactcag-cactcagttgctctgtcttaattcaataagctcgtttgatctccc-ttgtccccggcagAAACCAGACTCATGGAGGCTAGCTTGCCAGACTATTGTAGGCAACAAAGAGAACTCTGGCAAG
upper sequence: GLYMA17G30770.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G481261_T01 (Zea mays), 3'ss of exon 5
caaaaccagcttcttagaaaggtccttttaattttttagggtgatatgatggtaagttttgaaattttatgatcttctaagctttcgccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAAAACTCTGGCAAG
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----gtaggcattggacactggac-----agcgcgcaatgttcactcagcactcagttgctctgtctta-actcgtttgatctccc-ttgtctctggcagAAACCAGACTCATGGAGGCTAGCTTGCCAGACTATTGTAGGCAACAAAGAGAACTCTGGCAAG
upper sequence: GLYMA17G30770.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g04240.t01 (Vitis vinifera), 3'ss of exon 4
caaaaccagcttcttagaaaggtccttttaattttttagggtgatatgatggtaagtttt----gaaattttatgat----cttctaagctttcgccattttaa---acagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAAAACTCTGGCAAG
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----gcatgatctctgatcttctccctctggacac--acaatcatatgaagtttcgttctctcagaatttgcctaatgcttcttcatcacttctttggttttgatgtacagAAACCTGAATCTTGGAGGCTTGCTTGCCAAACTATTGTTGGAAATAAAGAGAACTCTGGCAAGMapped 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|213601734|gb|DB980935.1|DB980935EST: AGGATCTTTTAAATGAAAGAACAAACACTGAACTCAGATAACTTAGTAAG AAACCCGAAGCGAGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAA
genomic: AGGATCTTTTAAATGAAAGAACAAACACTGAACTCAGATATCTTAGTAAGgcatgttctc ... ttttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAA
EST:
gi|213613529|gb|DB963259.1|DB963259EST: AGGATCTTTTAAATGAAAGAACAAACACTGAACTCAGATATCTTAGTAAG AAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAA
genomic: AGGATCTTTTAAATGAAAGAACAAACACTGAACTCAGATATCTTAGTAAGgcatgttctc ... ttttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgatggtaagttttgaaattttatgatcttctaagctttcgccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAAAACTCTGGCAAG
ccatttt CT-rich tract
taagttttgaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaaaccagcttcttagaaaggtccttttaattttttagggtgatatgatggtaagttttgaaattttatgatcttctaagctttcgccattttaaacagAAACCCGAATCTTGGAGGCTGGCTTGTCAAACTATTGTTGGAAACAAAGAAAACTCTGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
caaaacc
- - - - gcttctt
- - - - - - - - - - - - - - - - - - - - -tgatatg