Sequence
atgc intronic sequence ATGC exonic sequence...ttttcatgtaaatcttaaattttttgtctatagcatctcatcttctgtcatgtttcatggaattacttttaataattttacaacaaaaaatgtatttcagGTTATGTATGCCTTTGTAATGCGTCCTGAGAGCTTGCCAAAATCCTATCAAGACTTCATTCAAAAGACCGGGCCAGTTGCAGAGCCTGTATACAAGGCTG
Basic information
species | Glycine max |
transcript | GLYMA20G34070.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g31260.1 (Oryza sativa), 3'ss of exon 4
ttttcatgtaaatcttaaattttttgtctatagcatctcatcttctgtcatgtttcatggaattacttttaataattttacaacaaaaaatgtatttcagGTTATGTATGCCTTTGTAATGCGTCCTGAGAGCTTGCCAAAATCCTATCAAGACTTCATTCAAAAGACCGGGCCAGTTGCAGAGCCTGTATACAAGGCTG
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-----gtaacaagatgaagttgaccgattt--gctttgggattattatcctgtt--atggagataagatctatataatcata-tgaaatatcc-ttccagGTTATGTATTCTTTCGTTATGAGGCCTGAAAGCTTACCTAAATCGTACCAAGACTTCATCCAAAAGACTGGACCAGTTGCGGAACCTGTTTACAAGGCTG
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G51150.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------ttttcatgtaaatcttaaattttttgtctatagcat-ctcatcttctgtcatgtttcatggaattacttttaat---------aattttacaacaaaaaatgtatttcagGTTATGTATGCCTTTGTAATGCGTCCTGAGAGCTTGCCAAAATCCTATCAAGACTTCATTCAAAAGACCGGGCCAGTTGCAGAGCCTGTATACAAGGCTG
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gtatttgagattcttctcttttcttcctgttctagttagtaatggagatagtatagacgttgaaagacatttttgtgtaccatacgtattctctccaatgtgatttggtagtgattatggtcagcaagctaattttgttgcaatgaggtcggtgcagGTTATGTATTCCTTTATAATGCGTCCTGAAACCTTGCCAAAATCATATAGAGAATTTATTCAGAAGACTGGTCCAGTTGCAAGGCCTGTCTACCAAGCTG
upper sequence: GLYMA20G34070.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0039g02700.t01 (Vitis vinifera), 3'ss of exon 4
-------ttttcatgtaaatcttaaattttttgtcta--tagcatctcatcttctgtcatgtttcatggaattacttttaataattttacaacaaaaaatgtatttcagGTTATGTATGCCTTTGTAATGCGTCCTGAGAGCTTGCCAAAATCCTATCAAGACTTCATTCAAAAGACCGGGCCAGTTGCAGAGCCTGTATACAAGGCTG
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acttcagttctctgttgtatctttgcatttctatcaaaatagtaactcagttactgac-ttttcattctagtcatatttcattggttgaatac--------tttttcagGTTATGTATGCCTTCATAATGCGTCCTGAGACCTTGCCCAAGTCATATCAAGATTTTATTCAGAAGACTGGGCCAGTTGCACAGCCTGTATACAAGGCTGMapped 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|151398679|gb|EV268550.1|EV268550EST: GTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG GTTATGTATGCCTTTGTAATGCGTCCTGAGAGCTTGCCAAAATCCTATCAA
genomic: GTCATTGGAGACATGGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAGgtattaataa ... tgtatttcagGTTATGTATGCCTTTGTAATGCGTCCTGAGAGCTTGCCAAAATCCTATCAA
EST:
gi|7796437|gb|AW781834.1|AW781834EST: GGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAG GTTATGTATGCCTTTGTAATGCGTCCTGAGAGCTTGCCAAAATCCTATCAA
genomic: GGAGATTCATTGCTGTTTGCCCTTGCTTGTGCACAGgtattaataa ... tgtatttcagGTTATGTATGCCTTTGTAATGCGTCCTGAGAGCTTGCCAAAATCCTATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcatgtttcatggaattacttttaataattttacaacaaaaaatgtatttcagGTTATGTATGCCTTTGTAATGCGTCCTGAGAGCTTGCCAAAATCCTATCAAGACTTCATTCAAAAGACCGGGCCAGTTGCAGAGCCTGTATACAAGGCTG
ttttaat putative branch site (score: 3)
aattacttttaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttcatgtaaatcttaaattttttgtctatagcatctcatcttctgtcatgtttcatggaattacttttaataattttacaacaaaaaatgtatttcagGTTATGTATGCCTTTGTAATGCGTCCTGAGAGCTTGCCAAAATCCTATCAAGACTTCATTCAAAAGACCGGGCCAGTTGCAGAGCCTGTATACAAGGCTG
- - catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa