Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgaaggttgctcaataagttggggtcattagttccacatgtaaattattatgcttttgccttgtcacttttaataatcccttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTTGTCATCAATACCCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
Basic information
species | Glycine max |
transcript | GLYMA06G43840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G014136_T01 (Zea mays), 3'ss of exon 2
gtatgtgaaggttgctcaataagttggggtcattagttccacatgtaaattattatgcttttgccttgtcacttttaataatcccttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTTGTCATCAATACCCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
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gtacgtgca--tagatt--tgggctaagcatact--ttttacg-gtataatctcactaactgtgctgattaagttctgttgctgtttct----ttgttacaaaagGTGCGAGGAATAGAAACAATAGCAACTTATGATTCAGAAACAAGAGAGTTCATCATAAATACTCCATGTGAATCAGCTCAGAAGTACTGGATTGGTGGAG
upper sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtgaaggttgctcaataagttggggtcattagttccacatgtaaattattatgcttttgccttgtcacttttaataatcccttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTTGTCATCAATACCCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
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----gtaggcatattttcttgatt----gccattttttttctccatatgtcatggtgatcttccacatttatattgagt---tctatttatttcttttgatatagGTACGGGGAATTGAAACAGTGACAACTTATGACCCAAAAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATTGGTGGGG
upper sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G06310.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgtgaaggttgctcaataagttggggtcat-tagttccacatgtaaattattatgcttttgccttgtcacttttaataatcccttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTTGTCATCAATACCCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
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----------------------gtaggcatattgcagtgtcattttgcatttatccag-----actatatatgtattggtgatctttgatttggtggctttca--gGTACGGGGAATTGAAACAGTGACTACTTATGACCCAACAACTGAAGAGTTTGTGATAAATACTCCTTGTGAATCTGCTCAGAAGTATTGGATCGGTGAGG
upper sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g02660.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtgaaggttgctcaataagttggggtcattagttccacatgtaaattattatgcttttgccttgtcacttttaataatcccttccagactaattttca---tagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTTGTCATCAATACCCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
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gtatgtgaaggttgtttgatcatttggttttgg-gccaccaggcctgtatgatgatgttctt-cattctccctgttgtttagttttcattggttctttcatgggtcagGTTCGAGGTATTGAAACAGTTACCACATATGACTCAAAAACTGGAGAGTTTGTTATTAACAGTCCCTGTGAATCAGCTCAGAAGTACTGGATAGGAGGAGMapped 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|192331590|gb|FK023437.1|FK023437EST: ATGATATCAAGGGTTGTTTTGCTATGTCTGAGTTAGGCCATGGAAGTAAT GTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTT
genomic: ATGATATCAAGGGTTGTTTTGCTATGTCTGAGTTAGGCCATGGAAGTAATgtatgtgaag ... attttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattatgcttttgccttgtcacttttaataatcccttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTTGTCATCAATACCCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
gactaat putative branch site (score: 2)
ttttcat CT-rich tract
tcacttttaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgaaggttgctcaataagttggggtcattagttccacatgtaaattattatgcttttgccttgtcacttttaataatcccttccagactaattttcatagGTTCGAGGAATTGAAACAGTCACTACTTATGATTCAAACACCGGAGAATTTGTCATCAATACCCCATGTGAATCGGGTCAGAAGTATTGGATTGGTGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG