Sequence
atgc intronic sequence ATGC exonic sequencegtgattttattgtactcatcaaacaatacatgcttgactactggtgtgctttattatcactcaattttgggaaggcttaacttgtagGAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTTCAAGATACTGTAAAAGAAATGGCAAAGGAGATTCAGAACTCACAAAGTG
Basic information
species | Glycine max |
transcript | GLYMA18G48050.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G48050.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g39550.3 (Oryza sativa), 3'ss of exon 3
-gtgattttattgtactcatcaaacaatacatgcttga-ctactggtg-tgctttattatcactcaatt---ttgggaagg-------cttaact-tgtagGAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTTCAAGATACTGTAAAAGAAATGGCAAAGGAGATTCAGAACTCACAAAGTG
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gtttaatttggtgtcccc-ttgtaccacctatactggaaccacaaaaactattgcagtgcaaatcgattggtttaagaatgtagttcactcatctgtgcagGAAGCGTTGAAAAGGAAACTGAAAGCAAGAATGGAGTATGCCAAGTTTTTGCAAGATACTGCAAAAGAAATGGCAAAGGAAGTTCAAACATCACGTAGTG
upper sequence: GLYMA18G48050.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g41950.1 (Oryza sativa), 3'ss of exon 3
-----------gtgattttattgtactcatcaaacaatacatgcttgactactggtgtgctttattatcactcaattttgggaaggcttaacttgtagGAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTTCAAGATACTGTAAAAGAAATGGCAAAGGAGATTCAGAACTCACAAAGTG
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gtactgaccaagacatgttatgata-tcttgccactgtatttgctaaa-tacaaacagattgactcaggtcaacattttttttttttgatacgtgcagGAGGCATTGAAAAGGAAATTGAAAGCAAGGATGGAATATGCAAGATTTTTACAAGATACTGCAAAAGAAATGGCAAAGGAAGTGCAGACGTCACGTAGTG
upper sequence: GLYMA18G48050.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G314656_T01 (Zea mays), 3'ss of exon 3
--------------gtgattttattgtactcatcaaacaatacatgcttgactactggtgtgctttattatcactcaattttgggaaggcttaacttgtagGAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTTCAAGATACTGTAAAAGAAATGGCAAAGGAGATTCAGAACTCACAAAGTG
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actgggtctcgtgtgccattttgt-gtcatgactacagagtaaatacattatcatagtgcaaactgattggctcaaggatatgattcattttactgtgcagGAAGCATTGAAGAGGAAACTAAAAGCAAGGATGGAATATGCAAAGTTTTTGCAAGATACAGCAAAAGAAATGGCAAAGGAAGTCCAAACATCACGTAGTG
upper sequence: GLYMA18G48050.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G65540.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------gtgattttat-----tgtactcatcaaacaatacatgcttgactactggtgtgctttattatcactcaattttggga---------aggcttaacttgtagGAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTTCAAGATACTGTAAAAGAAATGGCAAAGGAGATTCAGAACTCACAAAGTG
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gtactgttaaaaaacctattttattgcttctctattccttatacgtcatttatttttatttttacattgatctgggaagtatgaattggtttgatctttcattctcg--cgctgtcactcttgcctgtttctcaagtatgaatctaaaattcacgtttattttgcagGAGGCTCTAAAAAGAAGGTTGAATGCAAGAATGGAATATGCTAAGTTTCTCCAAGATACTGTCAAAGAAATGGCAAAGGAAGTCCAAACCTCTCGCAGTGMapped 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|14205472|gb|BG839150.1|BG839150EST: TATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAG GAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTT
genomic: TATTTCCCAACATGCTGCCTTCCACTTTCCAGGACAAGATGAAAGAACAGgtgattttat ... taacttgtagGAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgactactggtgtgctttattatcactcaattttgggaaggcttaacttgtagGAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTTCAAGATACTGTAAAAGAAATGGCAAAGGAGATTCAGAACTCACAAAGTG
gcttaac putative branch site (score: 3)
tttattatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattttattgtactcatcaaacaatacatgcttgactactggtgtgctttattatcactcaattttgggaaggcttaacttgtagGAGGCATTGAAAAGAAGGTTAAATGCAAGAATAGAATATGCCAAGTTTCTTCAAGATACTGTAAAAGAAATGGCAAAGGAGATTCAGAACTCACAAAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT