Sequence
atgc intronic sequence ATGC exonic sequence...ataaacatatcatacatggttgaatgataatgccaatacatacactatttgctctatgtttattggggtgttaatattttcatattcattgttgaacaggAATGGAGCTACCTCAGGGGTGGTCTAACTACTCTTGATCGTGATTATGGATGGATCAATAACATTCACCATGACATTGGCACTCATGTCATTCATCACCT
Basic information
species | Glycine max |
transcript | GLYMA18G43210.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G43210.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g18070.1 (Oryza sativa), 3'ss of exon 6
ataaacatatcatacatggttgaatgataatgccaatacatacactatttgctctatgtttattggggtgttaatattttcatattcattgttg----aacaggAATGGAGCTACCTCAGGGGTGGTCTAACTACTCTTGATCGTGATTATGGATGGATCAATAACATTCACCATGACATTGGCACTCATGTCATTCATCACCT
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--cattttcctacgtagaatgaagtgcagattatcaaatacttttcactattttggagtttat-atatttttaatgagctcacattttcttttgctctattagGAGTGGAGCTATCTGCGCGGAGGATTGACAACACTTGATCGGGACTACGGGTGGATCAACAACGTACACCATGACATTGGAACCCATGTCATTCATCATC-
upper sequence: GLYMA18G43210.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G129209_T01 (Zea mays), 3'ss of exon 3
ataaacatatcatacatggttgaatgataatgccaatacatacactatttgctctatgtttattggggtgttaatattttcatattcattg--ttgaacaggAATGGAGCTACCTCAGGGGTGGTCTAACTACTCTTGATCGTGATTATGGATGGATCAATAACATTCACCATGACATTGGCACTCATGTCATTCATCACCT
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--------------------------gtagtat--atagctaaatcaca-gctgcatgcaggtttcagt--taactgttctataactaatggacctactagGAATGGACCTATCTTCGGGGTGGCCTGACAACGCTCGACCGGGACTACGGGTGGATCAACAACATCCACCATGACATTGGGACTCATGTCATCCACCATC-
upper sequence: GLYMA18G43210.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0105g00430.t01 (Vitis vinifera), 3'ss of exon 6
--ataaacatatcatacatggttgaatgataatgccaata-catacactatttgctctatgtttat-tggggtgttaatattttcatattcattgttgaacaggAATGGAGCTACCTCAGGGGTGGTCTAACTACTCTTGATCGTGATTATGGATGGATCAATAACATTCACCATGACATTGGCACTCATGTCATTCATCACCT
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aaacagagggagaa-ataccaccaactgttaccttctctggtttaaacctttagcattgttttgatgtaaaaagtttgaattttcgttcttgtg--tggacagGAATGGAGTTATCTGAGGGGAGGGCTTACAACCCTTGATCGTGACTATGGATGGATTAATAACATTCACCATGATATTGGAACACATGTGATTCACCATC-
upper sequence: GLYMA18G43210.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ20170 (Selaginella moellendorffii), 3'ss of exon 6
-ataaacatatcatacatggttgaatgataatgccaatacatacactatttgctctatgtttattggggtgttaatattttcatattcattgttgaaca-----ggAATGGAGCTACCTCAGGGGTGGTCTAACTACTCTTGATCGTGATTATGGATGGATCAATAACATTCACCATGACATTGGCACTCATGTCATTCATCACCT
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catggccac-taccagaaagtaccatggtatcgtgggaaggtaca--agtattttcctgtt--ctgaggattcatttctctcaaacgagctcttttacatctcagGAATGGAATTACATCCGAGGCGGCCTATCAACTATAGACCGAGACTATGGATTGTTCAATAACATTCACCACGACATTGGAACGCATGTCGTGCATCATT-Mapped 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|305377701|gb|HO651932.1|HO651932EST: TTTGCACCATCATGGCCATGAAGACAAATTACCTTGGTACCGTGGAAAGG AATGGAGCTACCTCAGGGGTGGTCTAACTACTCTTGATCGTGATTATGGAT
genomic: TTTGCACCATCATGGCCATGAAGACAAATTACCTTGGTACCGTGGAAAGGtatccttcat ... gttgaacaggAATGGAGCTACCTCAGGGGTGGTCTAACTACTCTTGATCGTGATTATGGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttgctctatgtttattggggtgttaatattttcatattcattgttgaacaggAATGGAGCTACCTCAGGGGTGGTCTAACTACTCTTGATCGTGATTATGGATGGATCAATAACATTCACCATGACATTGGCACTCATGTCATTCATCACCT
tgttaat putative branch site (score: 3)
ttaatattttcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaacatatcatacatggttgaatgataatgccaatacatacactatttgctctatgtttattggggtgttaatattttcatattcattgttgaacaggAATGGAGCTACCTCAGGGGTGGTCTAACTACTCTTGATCGTGATTATGGATGGATCAATAACATTCACCATGACATTGGCACTCATGTCATTCATCACCT
- - - - - catacat
- - - - - - - - - - tgaatga
- - - - - - - - - - - - - - aatgcca
- - - - - - - - - - - - - - - - - - - catacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgtt