Sequence
atgc intronic sequence ATGC exonic sequence...tctgcatatagttgaatgcattataaatttgtggtgaatatttttctgctgtgtttaatgctttcttttcagctgagataactattgctcggtgtttcagGGCTTTGCAAATTGCGCTGTTTCCCACCTGTTGCACTTGCTTGGGATGATACATCTGGTCTTCATGTATATCCAAATTTGAACAGTGAGACAATTGTTGT
Basic information
species | Glycine max |
transcript | GLYMA16G06860.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G06860.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G27325.2 (Arabidopsis thaliana), 3'ss of exon 13
--------------------------------------------------------------------------tctgcatatagttgaatgcatt------ataaatttgtggtgaatatttttctgctgt---gtttaatgctttcttttcagctg------------agataactattgctcggtgtttcagGGCTTTGCAAATTGCGCTGTTTCCCACCTGTTGCACTTGCTTGGGATGATACATCTGGTCTTCATGTATATCCAAATTTGAACAGTGAGACAATTGTTGT
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gtgagtattccaaaccctctctttaatcatagaggtctttcttttagttttgtctgttaatcttctagtcagcatctgc-cgtaatttcctgttcttttggaataacataatagtcttcactcttcagttcttaagcttaaagattgtcattcccctatcgatgttataaatctgatcattgttcaat-tttcagAGCTCTGCAAATTGCGTTGTTTCCCACCTGTTGCTCTTGCCTGGGATTCTGCTTCTGGACTTCACGTTTTTGCAAATCTATACAGTGAGACAATAGTTAT
upper sequence: GLYMA16G06860.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0047g01140.t01 (Vitis vinifera), 3'ss of exon 8
tctgcatatagttgaatg-cattataaatttgtggtgaatatt-tttctgctgtgtttaatgct-ttcttttcagctgaga-taactattgctcggtgtttcagGGCTTTGCAAATTGCGCTGTTTCCCACCTGTTGCACTTGCTTGGGATGATACATCTGGTCTTCATGTATATCCAAATTTGAACAGTGAGACAATTGTTGT
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----tgaagggttggttgatgttatgttccggggaataaaatcatttccacaccccccatccctctttttttctgttaattcttgctctttcctgacaatgaagGGCTTTGCAAACTGCGCTGTTTCCCACCTGTAGCACTTGCTTGGGATACTACATCAGGTCTTCATGTGGTTCCAAATTTGTATGGGGAGACTATTGTGGTMapped 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|7588503|gb|AW704359.1|AW704359EST: GAGGAAGCCGGAGACCTTGAAAGTAGTA GGCTTTGCAAATTGCGCTGTTTCCCACCTGTTGCACTTGCTTGGGATGATA
genomic: GAGGAAGCCGGAGACCTTGAAAGTAGTAgtaagaattc ... ggtgtttcagGGCTTTGCAAATTGCGCTGTTTCCCACCTGTTGCACTTGCTTGGGATGATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgctgtgtttaatgctttcttttcagctgagataactattgctcggtgtttcagGGCTTTGCAAATTGCGCTGTTTCCCACCTGTTGCACTTGCTTGGGATGATACATCTGGTCTTCATGTATATCCAAATTTGAACAGTGAGACAATTGTTGT
agataac putative branch site (score: 3)
ataactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgcatatagttgaatgcattataaatttgtggtgaatatttttctgctgtgtttaatgctttcttttcagctgagataactattgctcggtgtttcagGGCTTTGCAAATTGCGCTGTTTCCCACCTGTTGCACTTGCTTGGGATGATACATCTGGTCTTCATGTATATCCAAATTTGAACAGTGAGACAATTGTTGT
- tgcatat
- - - - - - -gaatgca
- - - - - - - - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - - - - - - - - -ctgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctattgc