Sequence
atgc intronic sequence ATGC exonic sequencegtacctgaaacaattctatgggctcaggcataatgttaataatattaatatatactattcaaaatttgtctttttgtttcctaatttgctaagcatcttctaaattttcatcataatcatctcttgtacaatgtttctctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCCGCATGCCTTAAAGCTA
Basic information
species | Glycine max |
transcript | GLYMA15G13640.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 11
gtacctgaaacaattctatgggctcaggcataatgttaataatattaatatatactat-tcaaaatttgtctttttgtttcctaatttgctaagcatctt----ctaaattttcatcataatcatctcttgtacaatgtttctctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCCGCATGCCTTAAAGCTA
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-----------gttgacataggctc---tatttagttgctcagctaattatagattgtctctatctttgtttcactttgaccaaaattgttccaaatcaaagaattaagctttacaaaatgtcattttttttataatgt--------agAATGTACCTCCTGCTCTACTTGTGCGATTTCTGAGGGAGCATCGTTCTGAATGGGCTGATCCTGGTGTTGATGCTTATTCTGCTGCTTCTTTGCGAGCCA
upper sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 11
----------------------gtacctgaaacaatt--ctatgggctcaggcataatg-ttaataatattaatatatactattcaaa-atttgtctttttgtttcctaatttgctaagcatcttctaaattttcatcataatcatctct-tgtacaatgttt--ctctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCCGCATGCCTTAAAGCTA
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gtttgtacatgcgctccattctgtatcatgtttgtttgcttgttagttcattttagttgcttgttagctgttaca-atactaaacaaacaatcttcatggtagttttccttgcataaagttgtttttgtggtacaattaaccttaccccgatgtacttcttttgatattgcagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGGTCTGAATGGGCTGATCCTGGCATCGATGCTTATTCTGTCGCCTCTTTGAGGGCCA
upper sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G003509_T02 (Zea mays), 3'ss of exon 10
--------------------gtacctgaaacaattctatgggctcaggcataatgttaataatattaatata-tactat-tcaaaatttgtctttttgtttcctaatttgctaagcatcttctaaattttcatcataatcatctct-tgtacaatgttt--ctctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCCGCATGCCTTAAAGCTA
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gtttgtacatgcactcaattttgttccaagctactttaccttgtagtccatttagctgcttgtgttgttacagtactaaatgaacaatcttcatggtagttttccttgcataaaatcgtttttatggtatagttaaccttgccccaatgtacttcttctgatattgtagAATGTGCCACCTGCTCTACTTGTGCGATTTTTGAGGGAGCATCGCTCTGAATGGGCTGACCCTGGTGTTGATGCTTATTCCGCTGCCTCTCTGAGGGCCA
upper sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------gtacctgaaacaattctatgggctcaggcataatgttaataatattaatatatactattcaaaatttgtctttttg-tttcctaatttgctaagcatcttctaaattttcatcataatcatctcttgtacaatgtttc--tctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCCGCATGCCTTAAAGCTA
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gtacatagaaagtctagacaaccttgtaaggtctattgatagtgaatgtatgctaatttgtggatgtccaacttctgttttatctctcaatgccaccccacaaatattatttgaatcttctgggttaacat-cactattgaaatatttgatatatccatatctgactgtttatttgaatctgcagAATGTTCCCCCTGCTTTACTTGTTCGATTCCTGAGAGAACACCGTTCTGAGTGGGCTGACTATGGTGTTGATGCTTATTCTGCTGCATGTCTTAAAGCTAMapped 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|8284059|gb|BE021618.1|BE021618EST: CAGCATTTGGAGGTGGGGTCTTGTGTGCCAAGGCATCAATGCTCCTGCAG AATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAG
genomic: CAGCATTTGGAGGTGGGGTCTTGTGTGCCAAGGCATCAATGCTCCTGCAGgtacctgaaa ... ttctctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAG
EST:
gi|15337439|gb|BI498095.1|BI498095EST: CAGCATTTGGAGGTGGGGTCTTGTGTGCCAAGGCATCAATGCTCCTGCAG AATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAG
genomic: CAGCATTTGGAGGTGGGGTCTTGTGTGCCAAGGCATCAATGCTCCTGCAGgtacctgaaa ... ttctctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagcatcttctaaattttcatcataatcatctcttgtacaatgtttctctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCCGCATGCCTTAAAGCTA
ttctaaa putative branch site (score: 2)
tgtttctct putative PPT
taaattttcatcataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctgaaacaattctatgggctcaggcataatgttaataatattaatatatactattcaaaatttgtctttttgtttcctaatttgctaagcatcttctaaattttcatcataatcatctcttgtacaatgtttctctacagAATGTTCCTCCTGCTTTGCTTGTTCGGTTTTTGAGGGAGCATCGATCAGAGTGGGCTGATTATGGAGTTGATGCATACTCTGCCGCATGCCTTAAAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT