Sequence
atgc intronic sequence ATGC exonic sequencegttaatacccctgaagtttttattcttcatgtattgtatttggggtggcaataatatacgtattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
Basic information
species | Glycine max |
transcript | GLYMA04G09080.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtatttggggtggcaataatatacg-tattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
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-------------gagaagccattcacagcgcaa-acacttgggtgtcttgtaatgtttactgttggtatttattatgagcaagaagccaag--aactg-acttgaatg---cttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGC
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtatttggggtggcaataatatacgtattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
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-----------ggaaaatgagctactcaatccccgggaatcccagaggggatt---taagtttccaaactagccctaaataaacaag-taatgactctggtttt--ctgttc--tccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
gttaatacccctgaagtttttattcttcatgtattgtatttggggtggcaataatatacgtattt-tgactggttatgtttaaattgtcttcttacttgtatttggattgat-ccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
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----------------ttttggttctatgctgtccaaagtgggagtggtaaccct-tgaatatttgttgccattggtatataaataaaca----agtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
gttaatacccctgaagtttttattcttcatgtattgtatttggg-gtggcaataatatacgtattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
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-------------gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttat------ctctgtttcacagttttcatcatttgtattc--------------agGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gttaatacccctgaagtttttattcttcatgtattgtatttggggtggcaataatatacgtattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
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--------------------------------------------------gtattgtcgctgttattgatggcca--ctggcattgtcg-ctgacgcgtgttt-------cccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC
upper sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gttaatacccctgaagtttttattcttcatgtattgtatttggggtggcaataatatacgtattttgactggttatgttta--aattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
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-----------------------------------------------------------gtattgtcgctgttattgatggccactggcattgttgctgacgcgtgattc---ccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGCMapped 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|193511053|gb|FK468952.1|FK468952EST: GGGGCTAATAATGGATCCTCATTGGTTGTAATGTCTAAAG GTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTA
genomic: GGGGTTAATAATGGATCCTCATTGGTTGTAATGTCTAAAGgttaataccc ... atccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTA
EST:
gi|193531412|gb|FK483294.1|FK483294EST: GCTGGGGCTAATAATGGATCCTCATTGGTTGTAATGTCTAAAG GTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTA
genomic: GCTGGGGTTAATAATGGATCCTCATTGGTTGTAATGTCTAAAGgttaataccc ... atccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTA
EST:
gi|208053243|gb|GD853576.1|GD853576EST: TAATAATGGATCCTCATTGGTTGTAATGTCTAAAG GTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTTCCATTT
genomic: TAATAATGGATCCTCATTGGTTGTAATGTCTAAAGgttaataccc ... atccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTT-CCATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
tcctttt CT-rich tract
ttatgtttaaattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatacccctgaagtttttattcttcatgtattgtatttggggtggcaataatatacgtattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAATGGATCAACAAAAAGTGGAGAGAAGGATTTTATGTCACTGCTATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA