Sequence
atgc intronic sequence ATGC exonic sequence...ctgaacctgcaaatacaaacgccgagctaaagattgtagttttgttccttgagcttattatgtttgtgaaatggaaagctaataaatcatattattttagTATGTTATCTTTCGGCGTGGCATTGGAATTGATCGAACAGCTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
Basic information
species | Glycine max |
transcript | GLYMA16G05180.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G05180.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g29550.1 (Oryza sativa), 3'ss of exon 5
----ctgaacctgcaaatacaaacgccgagctaaagattgtagttttgttccttgagcttattatgtttgtgaaatggaaagctaataaatcatattattttagTATGTTATCTTTCGGCGTGGCATTGGAATTGATCGAACAGCTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
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tttattacacttgcctgtcccacaaggacagtaagtcatttttttctgctaatgctggagaatattcttattttattttacactggc----cacatttttgcagTATATTATCTTTCGTCGGGGCATTGGAATTGACCGTACAACCGATTACTTTATCATGGAGAAACTGGATGTGATCATATCCCGAGCTTGGAGCTCATTGC
upper sequence: GLYMA16G05180.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G011136_T03 (Zea mays), 3'ss of exon 5
--------------------------------------------------------ctgaacctgcaaatacaaacgccgagctaaagattgtagttttgttcc--ttgagcttattatgtttgtgaaatggaaagctaataaatcatattattttagTATGTTATCTTTCGGCGTGGCATTGGAATTGATCGAACAGCTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
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gtattattcgttcatgcaacttttcttttcatcctgatgatacttatgtttatgagggatgattagaaatctaca-atagcattggatgttttcatcatcctctgttttttctcatggt-ttcctaagacacattcttcattgtccacatc-ttgtagTATATCATCTTTCGTCGGGGCATTGGAATTGATCGAACAACTGACTACTTTTTCATTGAGAAAGTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGC
upper sequence: GLYMA16G05180.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G527387_T01 (Zea mays), 3'ss of exon 5
-ctgaacctgcaaatacaaacgccgagctaaagattgtagttttgttccttgagcttattatgtttgtgaaatggaaagcta-ataaatcatattattttagTATGTTATCTTTCGGCGTGGCATTGGAATTGATCGAACAGCTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
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aatttgtttgcttgttctaattttgtcttcacaagtattatttcctcggt--attttattatagttttcagcagttatttcacgtcaccaacatctttacagTATATTATCTTCCGTCGGGGCATTGGGATTGATCGGACAACTGACTACTTCTTCATGGAGAAAGTGGATGTCATCATATCCCGAGCATGGAGGTCATTGC
upper sequence: GLYMA16G05180.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
ctgaacctgcaaatacaaacgccgagctaaagattgtagttttgttccttgagcttattatgtttgtgaaatggaaagctaata-------aatcatattattttagTATGTTATCTTTCGGCGTGGCATTGGAATTGATCGAACAGCTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
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------atgcaa-tcttcatacaatgcagttaaccttcctcctcctcctctctctctctctcccaaaaagaagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTTMapped 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|209700073|gb|BW656229.1|BW656229EST: AATATTTTGAAGAGCATCATCATGATGACCTTCCTGATTTTTCTGATAAG TATGTTATCTTTCGGCGTGGCATTGGAATTGATCGAACAGCTG
genomic: AATATTTTGAAGAGCATCATCATGATGACCTTCCTGATTTTTCTGATAAGgtatggcttt ... attattttagTATGTTATCTTTCGGCGTGGCATTGGAATTGATCGAACAGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttgagcttattatgtttgtgaaatggaaagctaataaatcatattattttagTATGTTATCTTTCGGCGTGGCATTGGAATTGATCGAACAGCTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
agctaat putative branch site (score: 3)
ttatttt putative PPT
aaagctaataaatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgaacctgcaaatacaaacgccgagctaaagattgtagttttgttccttgagcttattatgtttgtgaaatggaaagctaataaatcatattattttagTATGTTATCTTTCGGCGTGGCATTGGAATTGATCGAACAGCTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - acctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt