Sequence
atgc intronic sequence ATGC exonic sequencegttagtgtcatccttaattcaggaaatatggattgactaaagtatacgttattagtgctcctgcacttactatctatatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
Basic information
species | Glycine max |
transcript | GLYMA02G39390.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 18
---gttagtgtcatccttaatt-caggaaatatggattgactaaagtatacgttattagtgctcctgcacttactatctatatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
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gtaatcaggaaagttttggagtatttcttacataactcttgcaaggtagttatttatatgggcgttgc-ttaacaattgttgtttgc-agATACAATGGCGTGCTCTTGATGAGATAAACTCTGGGGTGTGTGATGGGATGACGTATGAAGAGATAAAGAAAGTTATGCCCGAGGAATTTGA
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 17
----------gttagtgtcatccttaattcagg-aaatatggattgactaaagtatacgttattagtgct----cctgcacttactatctatatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
||| | | || ||| | || | ||| || || | | | ||| | || | ||| | | | | | |||||||||||||| ||||||||||| ||||| ||||| | |||||||||||||||||||| ||||| ||||| | | || || || |||||
gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os03g18310.3 (Oryza sativa), 3'ss of exon 16
----------gttagtgtcatccttaattcagg-aaatatggattgactaaagtatacgttattagtgct----cctgcacttactatctatatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA--------
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gtcagtttgctctaggaaattaccaaactcaagtaagaaaattttgtctcaacttttagctatcaaacctgacactggcatgttttccatgtgtcctctagATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAGTACGCAA
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 18
gttagtgtcatccttaattcaggaaa--tatggattgactaaagtatacgttattagtgctcctgcacttactatctatatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
|| | | | ||| |||| | | | ||| | || || | || || || | | | | |||||||||||||| || ||||||||||| ||| |||| ||||||||||||||||| |||||||| || ||||| | |||||| ||||| | |||
-gtatttggttacacgatttaggagtcttcttaaagaactgttgc-tatgtaagtacagcaagattgctcgacttgtgttatttgtagATACAATGGCGTGCTCTTGATGAGATCAATTCTGGAGTGTGTGATGGGATGACTTATGAAGAGATAAAGAAAATCATGCCCGAGGAATTTGA
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 16
gttag-tgtcatccttaattcaggaaatatggattgactaaagtatacgt-tattagtgct-cctgcacttac---tatctatatatgt-----tagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
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gttagctatcataggtgataaaataggcctagcaagactgctctctacttatagaagtgttaccaaaactaacttgtttctcctcatgttcttctagATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGA
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 18
gttagtgtcatccttaattcaggaaatatggattgact---aaagtatacgttatt--agtgctcctgcacttactatctatat----atgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
||| |||| ||| || | ||| | ||||| | || || |||| ||| | | | |||| || |||| | |||||||| || || || ||||| |||||||| || |||||||||||||| |||||||| | ||||||||||||||||| || || ||
gttggtgtttacctactgtccg--aatgtcttctgactcttgaggtgtataatattttgttgcgaggaaatcgatttctcatattttcatcttagGTGCAATGGCGTGCCCTGGACGAGATCAATGCTGGAGTTTGTGATGGGATGACATATGAAGAGGTAAAGAAGAACATGCCAGAAGAATACGA
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 18
----------------gttagtgtcatccttaattcaggaaatatggattgactaaagtatacgttattagtgctcctgcacttactatctatatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
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tagcttttgaatttagaaaaatttggtggataaccaacaaatctaggaatttgtgtggaaatgagtatagaaaattctataact--tttttacttttggtagATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAMapped 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|17024057|gb|BM095091.1|BM095091EST: CACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG ATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAG
genomic: CACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAGgttagtgtca ... tatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgactaaagtatacgttattagtgctcctgcacttactatctatatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
cacttac putative branch site (score: 2)
ttactatctatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgtcatccttaattcaggaaatatggattgactaaagtatacgttattagtgctcctgcacttactatctatatatgttagATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG