Sequence
atgc intronic sequence ATGC exonic sequencegtattcttttgcatctgtctacagtcatatacagagttagtttcagtcagcttaatgatatgcactttttgcagGTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATTGGATCTGCTAATATTAATGATAGGAGCTTACTTGGCTCCAGAGATTCTG
Basic information
species | Glycine max |
transcript | GLYMA09G04620.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 14
---------------------------------gtattcttttgcatctgtctacagtca-tatac------agagtta-gtttcagtcagctta-atgatatgcactt---tttgcagGTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATTGGATCTGCTAATATTAATGATAGGAGCTTACTTGGCTCCAGAGATTCTG
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gtaaagtatgagtcttgtccatttctggagcatgttttgttttctgccagggtcctggcactttgccatttaagagttgtgattcaaagaattagcatgtaaaatatttggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATTGGATCAGCTAACATAAATGATAGAAGCTTGCTTGGATCAAGAGATTCTG
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 14
----------------------gtattcttttgcat---ctgtctacagtcatatacagagttagtttcagtcagcttaatgata-tgcactttttgcagGTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATTGGATCTGCTAATATTAATGATAGGAGCTTACTTGGCTCCAGAGATTCTG
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tttgacccttgacatatgcgaaatgtcttataaaatagactgggaggagcagcatataaaatgtattcaggataccattctaacaatgtcccatttccagATTTATGTACATAGCAAGTTAATGATAGTTGATGACCGCATCACATTGATTGGCTCAGCTAATATTAATGATAGAAGCTTGCTTGGATCAAGAGACTCCG
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 15
lower sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 15
--------------------------------------------------------------------------gtattcttttgcatctgtctacagtcatatacagagttagtttcagtcagcttaatgatatgcactttt-----tgcagGTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATTGGATCTGCTAATATTAATGATAGGAGCTTACTTGGCTCCAGAGATTCTG
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gtaacaactcaatcatccagggtttagatttgtgcattgctgcctttttttttgtgatcacggaatcatataggatgccctgttatacatgtgcttgaatgcagtggtagtgagtattaaaaatgtgaatgctatttttttctctcaatgcagGTGTATGTTCACAGTAAAATCATGATAGTTGATGACCGTGCTGCATTGATTGGATCTGCCAATATTAACGACCGGAGTTTGCTTGGCTCAAGAGATTCTG
upper sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 16
------------------------------------------------------------------------------------------------gtattcttttgcatctgtctacagtc-atatacagagttagtttcagtc---agcttaatgatatg-cactttt----------------------tgcagGTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATTGGATCTGCTAATATTAATGATAGGAGCTTACTTGGCTCCAGAGATTCTG
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gtattgtgttttgctgatgcacataatcacatatgtacatttattttcaatgttccctaatcaattacaaaatctatttgtatgcatctttttcatgtttttttttttaaatttttataatggacatgggaaaaacaattgagcttggaactcagtggtatatcatttttcacattatattcctattgtttctgtagGTGTATGTGCATAGCAAAATCATGATAGTTGATGACTGCACAACCTTGATTGGATCCGCTAACATTAATGATAGGAGTTTGCTTGGATCAAGAGATTCTGMapped 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|151393683|gb|EV263558.1|EV263558EST: TAAGGTCTTATGGTAGACTCTCTAATGGTGGCCCTGTGGCAACCAGCCAG GTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATT
genomic: TAAGGTCTTATGGTAGACTCTCTAATGGTGGCCCTGTGGCAACCAGCCAGgtattctttt ... ctttttgcagGTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacagtcatatacagagttagtttcagtcagcttaatgatatgcactttttgcagGTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATTGGATCTGCTAATATTAATGATAGGAGCTTACTTGGCTCCAGAGATTCTG
gcttaat putative branch site (score: 4)
cacttttt putative PPT
ttaatgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcttttgcatctgtctacagtcatatacagagttagtttcagtcagcttaatgatatgcactttttgcagGTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATTGGATCTGCTAATATTAATGATAGGAGCTTACTTGGCTCCAGAGATTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT