Sequence
atgc intronic sequence ATGC exonic sequence...catatgccaacacatcagcaaagtatgggcattttggttatttccaatcattgttagggccttgtttgtataaatataaatgattgttaatgataatcagGTAATGGTATAGAAGAAAACAACTGAAGAGAAATTTCCTTCTATGAAGAAATATTCTGATAAGGCTCCTCCAAAGGATAAATTTGGTAAACATGAAGTCA
Basic information
species | Glycine max |
transcript | GLYMA06G37470.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G37470.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g63920.1 (Oryza sativa), 3'ss of exon 5
-------catatgccaacacatcagcaaagtatgggcattttggttatttccaatcattgttagggccttgtttgtata-aatataaatgattgttaatgataatcagGTAATGGTATAGAAGAAAACAACTGAAGAGAAATTTCCTTCTATGAAGAAATATTCTGATAAGGCTCCTCCAAAGGATAAATTTGGTAAACATGAAGTCA
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gtggggtgttgttttcttaaattcatgtaatgttttttttttcagttagagaaatttatattaattctggttcagtttgcaatttggtctgacgtctttg-tgaacagGTGTGGGTCTATAAGAAAACATCTGAGGAGAAATTCCCCACTTTGAAGAAGTATTCTGATAAGGCTCCTGCAAGTGATAAATTTGCATCTCATGAAGTCA
upper sequence: GLYMA06G37470.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G137968_T03 (Zea mays), 3'ss of exon 3
----catatgccaacacatcagcaaagtatgggcattttggttatttccaatcattgttagggccttgtttgtataaatataaatgattgttaatgataatcagGTAATGGTATAGAAGAAAACAACTGAAGAGAAATTTCCTTCTATGAAGAAATATTCTGATAAGGCTCCTCCAAAGGATAAATTTGGTAAACATGAAGTCA
||| | ||| | | | || || || | | | || | ||| || | | || || | || |||| |||| ||| || ||||||||| |||| || ||||| || || ||||||| ||||| || || ||||||||||| |||||||||| | ||||||||||
gcttcattttgcaaggttttttgagactagatttgaggtgattgtgttagcatgtccatattac-ttgcaatcatggctg-atataat-gcccttgttaat-agGTGTGGGTTTATAAGAAAACAGCTGAGGAAAAATTCCCCACTTTGAAGAAGTATTCGGACAAAGCTCCTCCAAATGATAAATTTGCTTCTCATGAAGTCA
upper sequence: GLYMA06G37470.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G137968_T02 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------catatgccaacacatca-gcaaagtatgggcattttggttatttccaatcattgt-----tagggccttgtt-tgtataaatataaatgat----tgttaatgataatcagGTAATGGTATAGAAGAAAACAACTGAAGAGAAATTTCCTTCTATGAAGAAATATTCTGATAAGGCTCCTCCAAAGGATAAATTTGGTAAACATGAAGTCA
|| | | ||| |||| || | | | | |||| | ||||| | | || | || | || || |||| || || |||| |||| ||| || ||||||||| |||| || ||||| || || ||||||| ||||| || || ||||||||||| |||||||||| | ||||||||||
gtaggcccagttcgtttgtcagttatacgctatattccatcatttacagaaatttataataatttaaatcttctgcttcattttgcaaggttttttgagactag--atttgaggtgattgtgttagcatgtccatattacttgcaatcatggctgatataatgcccttgttaat-agGTGTGGGTTTATAAGAAAACAGCTGAGGAAAAATTCCCCACTTTGAAGAAGTATTCGGACAAAGCTCCTCCAAATGATAAATTTGCTTCTCATGAAGTCA
upper sequence: GLYMA06G37470.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0048g00930.t01 (Vitis vinifera), 3'ss of exon 4
catatgccaacacatcagcaaagtatgggcattttggttatttccaatcattgttagggccttgtttgtataaatataaatg-attgttaatgataatcagGTAATGGTATAGAAGAAAACAACTGAAGAGAAATTTCCTTCTATGAAGAAATATTCTGATAAGGCTCCTCCAAAGGATAAATTTGGTAAACATGAAGTCA
|| || ||| | | | | | | |||||| || | | || || || | | | || || | ||||| ||| || |||||||| |||| |||| || || || ||||| ||||||||||| |||||||||||| |||||||||| | ||||| || |
cac-cattgcaacttcatgcatacaagtgtaacatcattatttgaaaaaaaaaaaaaaaaaactttgaaattcattttgttccaactttgatatggactagGTATGGGTTTACAAGAAAACGGCTGAGGAGAGGTTCCCCACTCTGAAGCAATATTCTGATCAGGCTCCTCCAACTGATAAATTTGCCACGCATGAGGTGAMapped 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|193407636|gb|FK374454.1|FK374454EST: ACTCCATTCTGTCTTTTT-CTCCTGCAAAGAAAAGGAACCTGTACTCAGG GTAATGGTATAGAAGAAAACA-CTGAAGAGAAATTTCCTTCTATGAAG
genomic: ACTCCATTCTGTCTTTTTTCTCCTGCAAAGAAAAGGAACCTGTACTCAGGgttggtggtg ... tgataatcagGTAATGGTATAGAAGAAAACAACTGAAGAGAAATTTCCTTCTATGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcattgttagggccttgtttgtataaatataaatgattgttaatgataatcagGTAATGGTATAGAAGAAAACAACTGAAGAGAAATTTCCTTCTATGAAGAAATATTCTGATAAGGCTCCTCCAAAGGATAAATTTGGTAAACATGAAGTCA
tgttaat putative branch site (score: 3)
ttgtttgtataaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catatgccaacacatcagcaaagtatgggcattttggttatttccaatcattgttagggccttgtttgtataaatataaatgattgttaatgataatcagGTAATGGTATAGAAGAAAACAACTGAAGAGAAATTTCCTTCTATGAAGAAATATTCTGATAAGGCTCCTCCAAAGGATAAATTTGGTAAACATGAAGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
-atatgcc
- - - - aacacat
- - - - - - - - - - - - - -ggcattt
- - - - - - - - - - - - - - - - - - - - - -ccaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatataa