Sequence
atgc intronic sequence ATGC exonic sequencegtaattccatgggacttgtattttagaatgaggccattccctatcagttctcttcattgtgactttgtagttatctgatcttgtttcttattgtagGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT
Basic information
species | Glycine max |
transcript | GLYMA13G02420.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 8
gtaattccatgggacttgtattttagaatgaggccattccctatcagttctcttcattgtgactttgtagttatctgatcttgtttcttat-tgtagGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT
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gtaacgtta--actcccctatcttgaaatttaaatttgacttgtagcttgaagtaaatgt----------ctgcttgaactggctcctttcatacagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGAC
upper sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g27950.1 (Oryza sativa), 3'ss of exon 8
gtaatt-ccatgggacttgtattttagaatgaggccattccctatcagttctcttcattgtgactttgtagttatctgatcttgtttcttattgt-agGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT
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gtaaatattctggaaacaacataaaactacttctggaagctccatcgtatgaaatctctagatgctaatattcatttttccctgcatctttttatcagAAATGTGAAATACCACGAGCCTGAGTTCTGGAAGTTTGGCGAAGACGGGAACAAGTATTTCCGCCATGCCACTGGGCAGATATATGCCATCTCAAAGGAC
upper sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 8
---gtaattccatgggacttgtattttagaatgaggccattccctatcagttctcttcattgtgactttgtagttatctga-tcttgtttcttattgtagGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT
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atgacaagtaatgtttgtttctacactgttacaaacatgagttcagacactagattgaagtattaattgaggcctgcttgaaccttctctattcatatagGAATGTTAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGAT
upper sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G070708_T02 (Zea mays), 3'ss of exon 8
gtaattccatgggacttgtattttagaatgaggccattccctatcagttctcttcattgtgactttgtagttatctgatcttgtttcttattgtagGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT
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----------gtaatgtttacttctacactgttacaacatgaattcaagcgctagatt-tgatagaggcctgcttgaacctgctctattcatatagGAATGTGAAGTACCATGAACCTGAGTACTGGAAATTTGGGGAGGAAGGAAATAAGTACTTCCGTCATGCTACAGGGCAGATATATGCCATTTCGAAAGAT
upper sequence: GLYMA13G02420.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G133613_T01 (Zea mays), 3'ss of exon 8
------gtaattccatgggacttgtattttagaat--gaggccattccct--atcagttctcttcattgtgactttgtagttatctgatcttgtttcttattgtagGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT
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gtataaattcctctgaaaaaaaagcagcgcagcattcgaattgaatcgtcgaaataccagccttcgttttgacatacatgttttct----ttttcccccacatcagGAATGCGAAATACCATGAGCCTGAGTTCTGGAAGTTCGGAGAGGACGGGAACAAGTACTTCCGCCACGCCACGGGGCAGATATACGCCATCTCCAAGGACMapped 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|151401991|gb|EV271804.1|EV271804EST: CCAAGGATCTACATTGGATGTATGAAATCTGGACCTGTTCTTTCTCGAAG GGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGGGGGGAA
genomic: CCAAGGATCTACATTGGATGTATGAAATCTGGACCTGTTCTTTCTCGAAGgtaattccat ... cttattgtagGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcagttctcttcattgtgactttgtagttatctgatcttgtttcttattgtagGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT
atctgat putative branch site (score: 4)
tcttgtttcttatt CT-rich tract
tttcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattccatgggacttgtattttagaatgaggccattccctatcagttctcttcattgtgactttgtagttatctgatcttgtttcttattgtagGGATGTCAAGTATCATGAACCTGAGTTTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT