Sequence
atgc intronic sequence ATGC exonic sequence...tattactaggttgtgtgctttagcttctccaagactggaatgttgatcttgtctttgtcatcaagcttttctgaatttatattgttccatgattcatcagGGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGTTGCAAACCATCCTGATGCGGGTGGAAGTCATTATCTTGCTTCCAAAATA
Basic information
species | Glycine max |
transcript | GLYMA05G16850.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G16850.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G040587_T01 (Zea mays), 3'ss of exon 3
-tattacta-ggttgtgtgctttagcttctccaagactggaatgttgatcttgtctttgtcatcaagcttttctg--aatttatattgttccatgattcatcagGGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGTTGCAAACCATCCTGATGCGGGTGGAAGTCATTATCTTGCTTCCAAAATA
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gtactagtgtggtcagtcattcttgagtttttataagtgt--cgctgcttagtgattaaacgtttttttttcatgctagcttataattattgatgtttc--cagGGAAACTGCCAACGCAGAGAAGGTAAAAGAGGCGCACAAGAGGGTTATGGTCGCCAACCATCCAGATGCTGGTGGAAGTCATTACCTTGCGTCAAAGATT
upper sequence: GLYMA05G16850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G35795.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------tattactaggttgtgtgctttagcttctccaa--gactggaatgttgatcttgtctttgtca-------tcaagcttttctgaatttatattgttccatgattcat----cagGGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGTTGCAAACCATCCTGATGCGGGTGGAAGTCATTATCTTGCTTCCAAAATA
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gtgaaggaaacacacacacatactctctctttctcttgtgtttagtagtttctcaatcctcaatgatcaatttggttatagcattagcatagtttccattgaagaaagtgtaacgttgtttgaaatgtggggttttgtgattgaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGTAGCAAACCATCCAGATGCAGGTGGTAGCCATTTCCTAGCCTCTAAGATC
upper sequence: GLYMA05G16850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g03880.t01 (Vitis vinifera), 3'ss of exon 2
tattactaggttgtgtgctttagcttctccaagactggaatgttgatcttgtctttgtcatcaagcttttctgaatttata--ttgttccatgattcatcagGGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGTTGCAAACCATCCTGATGCGGGTGGAAGTCATTATCTTGCTTCCAAAATA
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--caactaatgcctgtcattttgaagtcatgtatcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgtttgtgggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATCMapped 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|19934531|gb|BQ079561.1|BQ079561EST: TTCCAATCTACAATGACAAGGAGAGAAGCAGCACTAATATTAGGCGTCAG GGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGT
genomic: TTCCAATCTACAATGACAAGGAGAGAAGCAGCACTAATATTAGGCGTCAGgtaacattga ... gattcatcagGGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGT
EST:
gi|19935102|gb|BQ080132.1|BQ080132EST: TTCCAATCTACAATGACAAGGAGAGAAGCAGCACTAATATTAGGCGTCAG GGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGT
genomic: TTCCAATCTACAATGACAAGGAGAGAAGCAGCACTAATATTAGGCGTCAGgtaacattga ... gattcatcagGGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttgtctttgtcatcaagcttttctgaatttatattgttccatgattcatcagGGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGTTGCAAACCATCCTGATGCGGGTGGAAGTCATTATCTTGCTTCCAAAATA
tgttgat putative branch site (score: 4)
ttttctgaatttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattactaggttgtgtgctttagcttctccaagactggaatgttgatcttgtctttgtcatcaagcttttctgaatttatattgttccatgattcatcagGGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGTTGCAAACCATCCTGATGCGGGTGGAAGTCATTATCTTGCTTCCAAAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - ggttgtg
- - - - - - - -tgcttta
- - - - - - - - - - - -cttctcc
- - - - - - - - - - - - - - - - - - ggaatgt