Sequence
atgc intronic sequence ATGC exonic sequencegtatgttcttgactgaattgcaagtttttgcagttgttgtatttgagtcaataaactagtggacattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCAAAGATCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCAC
Basic information
species | Glycine max |
transcript | GLYMA19G43400.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgttcttgactgaattgcaagtttttgcagttgttgta-tttgagtcaataaactagtggacattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCAAAGATCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCAC
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--------------gtagtatacagataaacagtttccgtactttgtgtgaatga-ttagt-----------tgtttactattgggattaata--tttgc----ttggatca----acttagGTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCACTGATAGGTTTGAGATGTGGGGAGATGGGCTTCAGACCCGTTCTTTTAC
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 3
gtatgttcttgactgaattgcaagtttttgcagttgttgtatttgagtcaataaactagtggacattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCAAAGATCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCAC
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------------------------------------------gtgagttcatagattga--gatcttcttctttcttcttt-agcctgagtgggagtaactgagattgtttcaaaac-cagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCTCTGACCTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCCTTCAC
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 3
gtatgttcttgactgaattgcaagtttttgcagttgttgtatttgagtcaataaactagtggacattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCAAAGATCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCAC
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------------------------------------------gtgacttcatagattga--gatcttcttctttcttcttt-agcttgagtgggagtaactgagattgtttcaatac-cagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCGTTCAC
upper sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ10353 (Selaginella moellendorffii), 3'ss of exon 3
gtatgttcttgactgaattgcaagtttttgcagttgttgtatttgagtcaataaactagtggacattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCAAAGATCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCAC
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------------------------------------------gtgagttcatagattga--gatcttcttct-tgcttctttagcctgagtgggagtaactgagattgtttcaaaac-cagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCTCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCCTTCACMapped 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|7232221|gb|AW567578.1|AW567578EST: CCGGATTGGGAGATTCCATAACATATATGGTCCTTATGGGACATGGAAGG GTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCA
genomic: CCGGATTGGGAGATTCCATAACATATATGGTCCTTATGGGACATGGAAGGgtatgttctt ... tgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCA
EST:
gi|298163054|gb|HO011787.1|HO011787EST: CCGGATTGGGAGATTCCATAACATATATGGTCCTTATGGGACATGGAAGG GTGGAAGGGAGAAGGCTCCTGCTACTTTTTGTCGCAAGACACTTACTTCCA
genomic: CCGGATTGGGAGATTCCATAACATATATGGTCCTTATGGGACATGGAAGGgtatgttctt ... tgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCAAAGATCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCAC
atttaac putative branch site (score: 3)
ttttgtc putative PPT
atttaacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttcttgactgaattgcaagtttttgcagttgttgtatttgagtcaataaactagtggacattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCAAAGATCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA