Sequence
atgc intronic sequence ATGC exonic sequence...tcttaattaagaagatactgtttttcattatttaaacattagaatatacatacgtactcaattaattaattatatatgttcctgtgtttgagaaatgcagATGGGCTCACATTGCAAGCCACTTACCAGGTAGAACTGACAACGAAATAAAGAACTACTGGAATTCTTGGATCAAAAAGAAAATTAGAAAGCCTTCTTCG
Basic information
species | Glycine max |
transcript | GLYMA01G43120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G43120.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g05520.1 (Oryza sativa), 3'ss of exon 2
-tcttaattaag--aagatactgtttttcattatttaaacat-tagaatatacatacg-tactcaattaattaattatatatgttcctgtgtttgagaaatgcagATGGGCTCACATTGCAAGCCACTTACCAGGTAGAACTGACAACGAAATAAAGAACTACTGGAATTCTTGGATCAAAAAGAAAATTAGAAAGCCTTCTTCG
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tgattaatttgaccaagatatgatggtgtgtagtatcagtatataaaccatagagagaataattaactaatta-taattaatgttgttgtctctctga----cagGTGGGCCCACATTGCCAGCCACCTGCCTGGCCGGACCGACAACGAGATCAAGAACTACTGGAATTCATGGATCAAGAAGAAGATTCGCAAGCCGGCGGCG
upper sequence: GLYMA01G43120.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G325907_T01 (Zea mays), 3'ss of exon 2
tcttaattaagaagatactgtttttcattatttaaacattagaatatacatacgtactcaat---taattaattata--tatgttcctgtgtttgagaaatgcagATGGGCTCACATTGCAAGCCACTTACCAGGTAGAACTGACAACGAAATAAAGAACTACTGGAATTCTTGGATCAAAAAGAAAATTAGAAAGCCTTCTTCG
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---tgaaaatgaaggctaaatccaaaggaatgcaacacctaggctagc--tagctagttgatgtgtacatgaccacagccatgtcccccggttctctctctgcagGTGGGCCCACATTGCCAGCCACTTGCCCGGGCGGACGGACAACGAGATCAAGAACTACTGGAACTCGTGGATCAAGAAGAAGATCCGGAAGCCGGCGATG
upper sequence: GLYMA01G43120.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g00320.t01 (Vitis vinifera), 3'ss of exon 2
-------tcttaattaagaagatactgtttttcattatttaaacattagaatatacatacgtactcaattaattaattatatatgttcctgtgtttgagaaatgcagATGGGCTCACATTGCAAGCCACTTACCAGGTAGAACTGACAACGAAATAAAGAACTACTGGAATTCTTGGATCAAAAAGAAAATTAGAAAGCCTTCTTCG
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ttcgtgaagttacttccaaacccaccgtatt-catgaactaatcac--aaactttgaggtgtttcagtcttcttaaggactgacatt----tgtttgggaattgtagATGGGCTCATATTGCAAGTCACTTGCCTGGAAGAACAGACAATGAGATAAAGAATTACTGGAATTCGTGGATCAAAAAGAAGATAAGGAAGCCGTCGGCA
upper sequence: GLYMA01G43120.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S24_48V6.1 (Physcomitrella patens), 3'ss of exon 2
-tcttaattaagaagatactgtttttcattatttaaacattagaatatacatacgtactcaattaattaattatatatgttcctgtgtttgagaaatgcagATGGGCTCACATTGCAAGCCACTTACCAGGTAGAACTGACAACGAAATAAAGAACTACTGGAATTCTTGGATCAAAAAGAAAATTAGAAAGCCTTCTTCG-
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ctagaaattgagattttccagacttttcttctattaatttcagcctaatcttgagcaatgagacattgagtaattt-ttttccttttcctgcacactgcagATGGTCGCAGATTGCGACGCAGCTTCCCGGTCGCACTGACAACGAAATAAAGAACTTCTGGAATTCCTGTATTAAGAAGAAG-TTACGCAACATCGGTATTMapped 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|192304167|gb|FG993493.1|FG993493EST: CCTGAAGAGGAGAAGTTAATTATAAGTCTTCATGGGGTCGTTGGCAACAG ATGGGCTCACATTGCAAGCCACTTACCAGGTAGAACTGACAACGAAATAAA
genomic: CCTGAAGAGGAGAAGTTAATTATAAGTCTTCATGGGGTCGTTGGCAACAGgtttgaatca ... agaaatgcagATGGGCTCACATTGCAAGCCACTTACCAGGTAGAACTGACAACGAAATAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacatacgtactcaattaattaattatatatgttcctgtgtttgagaaatgcagATGGGCTCACATTGCAAGCCACTTACCAGGTAGAACTGACAACGAAATAAAGAACTACTGGAATTCTTGGATCAAAAAGAAAATTAGAAAGCCTTCTTCG
aattaat putative branch site (score: 3)
tactcaattaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttaattaagaagatactgtttttcattatttaaacattagaatatacatacgtactcaattaattaattatatatgttcctgtgtttgagaaatgcagATGGGCTCACATTGCAAGCCACTTACCAGGTAGAACTGACAACGAAATAAAGAACTACTGGAATTCTTGGATCAAAAAGAAAATTAGAAAGCCTTCTTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
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- - - - - - -gatactg
- - - - - - - - - - - - - - - - - - - - - - - tacatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtttg