Sequence
atgc intronic sequence ATGC exonic sequencegtaatgaatctttctaccttttttcagtgatagtttaaattattaagcaaaaccaccacctgtcccccgaataactgaaaggacccttaagatagttccatttttattaactggaagttgtgaaaaatgtcagGGACTGGTGAATTTAAATTTCTTGCAAGAGAAAAAGGAAGCAGACTTTCGTTATGGACTTGTGCGGGTTCGGGAAAATGCTGAATCAATTGCTTTCTACA
Basic information
species | Glycine max |
transcript | GLYMA08G17110.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g11946.1 (Oryza sativa), 3'ss of exon 4
gtaatgaatctttctaccttttttcagtgatagtttaaattattaagcaaaaccaccacctgtcccccgaata-actgaaaggacccttaagatagttccatttttattaactggaagttgtgaaaaatgtcagGGACTGGTGAATTTAAATTTCTTGCAAGAGAAAAAGGAAGCAGACTTTCGTTATGGACTTGTGCGGGTTCGGGAAAATGCTGAATCAATTGCTTTCTACA
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----------------------------------gtaagttgcttatcaa---cattatttatctccaacttgcattgaacatactctttcttt--ctttaaaactaattgctggctattcttgtacg-gacagAATTTGGTCAACTTGAACTTCATGCAAGAAAAGAAAGAAGCAGATTTTCGTTATGGACTTGTCCGAGTTAGAGAAAATGCTGAATCAATTGCTTTTTATG
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54350.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgaatctttctaccttttttcagtgatagtttaaattattaagcaaaaccaccacctgtcccccgaataactgaaaggacccttaagatagttccatttttattaactggaagttgtgaaaaatgtcagGGACTGGTGAATTTAAATTTCTTGCAAGAGAAAAAGGAAGCAGACTTTCGTTATGGACTTGTGCGGGTTCGGGAAAATGCTGAATCAATTGCTTTCTACA
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--------------------------gtacaacaatgcctcgttaagcagtgtgattgtctctattctgttccgcttcaga---ttttggctttgttgcattaacattccct----cttgtgt------tcagGGACTAGTGAATCTCAACTTTCTACAAGAGAAGAAAGAGGCTGACTTTCGTTACAGCCTTGTACGAGTGAGGGAAAATGCTGAATCTATTGCTTTCTATG
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0085g01190.t01 (Vitis vinifera), 3'ss of exon 4
gtaatgaatctttctaccttttttcagtgatagtttaaattattaagcaaaaccaccacctgtcccccgaataactgaaaggacccttaagatagttccatttttattaactggaagttgtgaaaaatgtcagGGACTGGTGAATTTAAATTTCTTGCAAGAGAAAAAGGAAGCAGACTTTCGTTATGGACTTGTGCGGGTTCGGGAAAATGCTGAATCAATTGCTTTCTACA
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----gtaattttcctacctttttgaaatcattattttgaatttgcagtgaaac-attat-----------gcaatagaacatattcttactccagt-caataggaaatattt--catctgtga----tttcagGGACTGGTAAACCTAAATTTCTTGCAAGAGAAGAAAGAAGCAGATTTTCGTTATGGACTTGTGCGTATTCGTGAAAATGCTGAATCAATTGCGTTCTATA
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S113_134V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaatgaatctttctaccttttttcagtgata-gtttaaattattaagcaaaaccaccacctgtcccccgaataactgaaaggacccttaagatagttccatttttattaactggaagttgtgaaaaatgtcagGGACTGGTGAATTTAAATTTCTTGCAAGAGAAAAAGGAAGCAGACTTTCGTTATGGACTTGTGCGGGTTCGGGAAAATGCTGAATCAATTGCTTTCTACA
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--------------------------gtggcccgtcgaagtagtttcactgcgtgattgcacttcacatttttcatcgcat---cacatggtgtaaatatactgataattacaagcaagtgtt-----ttgcagAACTTGGTGGGTCTTAATTTTATGCAAGAAAAGAAGGAAGCCGATTTTCGGTATGGATTAGTTCGCGTACGTGAAAATGCAGAATCGATTGCTTTCTACGMapped 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|13311631|gb|BG405282.1|BG405282EST: TTATCGTATACTCGATTGGTGGGACAGCTATCAGTGTTTTCCTTGGAAGA GGACTGGTGAATTTAAATTTCTTGCAAGAGAAAAAGGAAGCAGACTTTCGT
genomic: TTATCGTATACTCGATTGGTGGGACAGCTATCAGTGTTTTCCTTGGAAGAgtaatgaatc ... aaaatgtcagGGACTGGTGAATTTAAATTTCTTGCAAGAGAAAAAGGAAGCAGACTTTCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggacccttaagatagttccatttttattaactggaagttgtgaaaaatgtcagGGACTGGTGAATTTAAATTTCTTGCAAGAGAAAAAGGAAGCAGACTTTCGTTATGGACTTGTGCGGGTTCGGGAAAATGCTGAATCAATTGCTTTCTACA
tattaac putative branch site (score: 1)
ttccatttttattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgaatctttctaccttttttcagtgatagtttaaattattaagcaaaaccaccacctgtcccccgaataactgaaaggacccttaagatagttccatttttattaactggaagttgtgaaaaatgtcagGGACTGGTGAATTTAAATTTCTTGCAAGAGAAAAAGGAAGCAGACTTTCGTTATGGACTTGTGCGGGTTCGGGAAAATGCTGAATCAATTGCTTTCTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG