Sequence
atgc intronic sequence ATGC exonic sequence...tatttttatatatttttcccctaaaagacatgcaattgcttattgacatgccttgaggtcaataattttatgtcatttttcatgtgaatgtgttccatagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
Basic information
species | Glycine max |
transcript | GLYMA02G45000.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 3'ss of exon 9
tatttttatatatttttcccctaaaagacatgcaattgcttattgacatgccttgaggtcaataat-tttatgtcatttttcatgtgaatgtgttccatagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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-----------gtgatgagcctgatttgtttcatatattgttttaataaatataaacg--aataacctctgacttgttctttttctatatatgtc----agGTTCTTGATCACCTAGTGATTCAGAAGCTAAATGCTGAGGGCAGGCTCGAGAAGAAAGAATCAAAAAAAGGTGGTTCCATGTTTGACAAG
upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G010342_T01 (Zea mays), 3'ss of exon 18
--tatttttatatatttttcccctaaaagacatgcaattgcttattgacatgccttgaggtcaataattttatgtcattttt-catgtgaatgtgttccatagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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ggaacgcgcaaagaaaaagatggttgtcaaagtgca-ttgttcat--gtattctttagtaggattattgaactgttctttttacctattgtttcctatttcagGTTCTTGATCACTTGGTTATTCAGAAGCTAAATGCTGAGGGCAGGCTTGAGAAGAAAGAATCCAAAAAGGGTGGCTCCATATTTGACAAG
upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G141258_T01 (Zea mays), 3'ss of exon 22
tatttttatatatttttcccctaaaa--gacatgcaattgctta-ttgacatgccttg-aggtcaataattttatgtcatttttcatgtgaatgtgttccatagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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--ttttggaacgcgcaaagaaaaagatggttgtcaaactgcatagttcatgtacttagtaggattattgaactgtactttttaccttttttatatatttca--gGTTCTTGATCACTTGGTCATTCAGAAGCTAAACGCTGAGGGCAGGCTTGAGAAGAAAGAATCCAAAAAAGGTGGCCCCATATTTGACAAG
upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 20
lower sequence: AT2G13370.1 (Arabidopsis thaliana), 3'ss of exon 21
-------tatttttatatatttttcccctaaaagacatgcaattgcttattgacatgccttgaggtcaataattttatgtcatttttcatgtgaatgtgttccatagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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agtcaatcacctgtggatgagataggttcaaa----acccaaatttttacttgtatcactttgttatagcaggctgtaactttttttcgtcca---ccattctctagGTTCTTGATCATTTGGTTATTCAAAAACTGAATGCGGAGGGTAGGCTGGAGAAGCGAGAAACTAAAAAAGGA---AGTAATTTTGACAAG
upper sequence: GLYMA02G45000.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 3'ss of exon 20
-----------------------------------------------------tatttttatatatttttcccctaaaagacatg------caattgcttattgacatgcc-----ttgaggtcaataattttatgtcatttttcatgtga----atgtgttcc--atagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
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gtaaaccaaacatttctttgtctatgcttaaatccttttcttttcatactgtttatatttaaaagcatgtctgtttgcacacatggtggattatatggtctctactatttcactaattgaggccaaacaatttacatgttttttcttatgttcccattttttctttatagGTACTTGATCATTTGGTGATTCAAAAACTAAATGCAGAAGGTAGACTGGAGAAGAAAGAATCGAAAAAGGGG---AGTTACTTTGACAAAMapped 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|16995860|gb|BM085232.1|BM085232EST: CAAGCAAAAGTGTTGAGGAAGATATTTTGGAACGTGCTAAGAAGAAAATG GTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAG
genomic: CAAGCAAAAGTGTTGAGGAAGATATTTTGGAACGTGCTAAGAAGAAAATGgtatgtttaa ... tgttccatagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatgccttgaggtcaataattttatgtcatttttcatgtgaatgtgttccatagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
tattgac putative branch site (score: 2)
aataattttatgtcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttttatatatttttcccctaaaagacatgcaattgcttattgacatgccttgaggtcaataattttatgtcatttttcatgtgaatgtgttccatagGTTCTGGACCACTTGGTGATTCAAAAGCTAAATGCAGAGGGTAGGCTGGAGAAGAAAGAAGCCAAAAAAGGAGGAAGTTATTTTGACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - tttcccc
- - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - tgcttat
- - - - - - - - - - - - - - - - - - - - - - - catgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaatg