Sequence
atgc intronic sequence ATGC exonic sequencegtatatatttctgtacttggaatgcattgtattgttgtcaccagtacaaagtgattatataggatgacattctgactcttggttcatctttagTGGCTACTGAGGTTTTTAGTTGGGGCAGTGGTGCAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGCAAAGTTGATTCACTTGG
Basic information
species | Glycine max |
transcript | GLYMA16G04300.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G04300.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G135133_T01 (Zea mays), 3'ss of exon 3
gta-tatatttctgtacttggaatgcattgtattgttgtcaccagtacaaagtgattatataggatgacattctgactcttggttcatctttagTGGCTACTGAGGTTTTTAGTTGGGGCAGTGGTGCAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGCAAAGTTGATTCACTTGG
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gtagctttcttctgccccaggaa---atggttctcttatatcgcgctcttggcaatt---tggcttgctttatggaagtttttttcat-tttagTTGCAACGGAAGTCTTCAGTTGGGGAAGTGGGACAAATTATCAGCTTGGAACTGGCAACGTCCACATACAAAAACTACCATGCAAAGTAGAAGCTTTGCA
upper sequence: GLYMA16G04300.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G03790.3 (Arabidopsis thaliana), 3'ss of exon 3
-------gtatatatttctgtactt----ggaatgcattg--tattgttgtcaccagtacaaa-gtgattatatagga--tgacattctgactcttggttcatctttagTGGCTACTGAGGTTTTTAGTTGGGGCAGTGGTGCAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGCAAAGTTGATTCACTTGG
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gtaactaatattttctctttgatctttaaggagaaccttaatcagtcttgacactttttcttacgcaacttttgagaagctgaaatgttggcttcatttttcttttcagTGGCTACAGAGGTTTTCAGCTGGGGAAATGGTGCAAACTACCAACTTGGAACTGGCAATCAACATGTTCAGAAGGTACCAGGGAGAGTTGATTCACTGCA
upper sequence: GLYMA16G04300.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G03790.1 (Arabidopsis thaliana), 3'ss of exon 3
-------gtatatatttctgtactt----ggaatgcattg--tattgttgtcaccagtacaaa-gtgattatatagga--tgacattctgactcttggttcatctttagTGGCTACTGAGGTTTTTAGTTGGGGCAGTGGTGCAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGCAAAGTTGATTCACTTGG---------
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gtaactaatattttctctttgatctttaaggagaaccttaatcagtcttgacactttttcttacgcaacttttgagaagctgaaatgttggcttcatttttcttttcagtggctacagAGGTTTTCAGCTGGGGAAATGGTGCAAACTACCAACTTGGAACTGGCAATCAACATGTTCAGAAGGTACCAGGGAGAGTTGATTCACTGCATGGTTGTTT
upper sequence: GLYMA16G04300.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0032g00280.t01 (Vitis vinifera), 3'ss of exon 4
gtatatatttctgtacttgg-aatgcattgtattgttgtcaccagtacaaagtgattatataggatgacattc-tgactcttggttcatctttagTGGCTACTGAGGTTTTTAGTTGGGGCAGTGGTGCAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGCAAAGTTGATTCACTTGG
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--gtg-gttattgcacttgtcaatttattgaatcat-gtggttgttggaaa----tctttagggataacctgagtgacttttcatgtctgtttagTTGCCACGGAGTTATTTAGTTGGGGAAGTGGTGTGAACTATCAACTTGGAACTGGGAACACTCACATACAAAAGCTACCATGCAAAGTTGATTCACTTCAMapped 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|193570725|gb|FK529464.1|FK529464EST: TCTCTTATCTGGCTCTGTATTTCAGGTTCTTCGAGATGAACACAGTTCAG TGGCTACTGAGGTTTTTAGTTGGGGCAGTGGTGCAAATTATCA
genomic: TCTCTTATCTGGCTCTGTATTTCAGGTTCTTCGAGATGAACACAGTTCAGgtatatattt ... tcatctttagTGGCTACTGAGGTTTTTAGTTGGGGCAGTGGTGCAAATTATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccagtacaaagtgattatataggatgacattctgactcttggttcatctttagTGGCTACTGAGGTTTTTAGTTGGGGCAGTGGTGCAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGCAAAGTTGATTCACTTGG
ttctgac putative branch site (score: 2)
ttcatcttt putative PPT
aaagtgattatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatatttctgtacttggaatgcattgtattgttgtcaccagtacaaagtgattatataggatgacattctgactcttggttcatctttagTGGCTACTGAGGTTTTTAGTTGGGGCAGTGGTGCAAATTATCAGCTTGGAACTGGAAATGCGCATATTCAGAAGTTACCATGCAAAGTTGATTCACTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG