Sequence
atgc intronic sequence ATGC exonic sequence...gtaggaattgtttgggttctcagtaggatttataaacatgcatggttaagcatttgtttgcttttgacatcttgtacaataattgttatttatgagtcagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCC
Basic information
species | Glycine max |
transcript | GLYMA19G17660.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G17660.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 7
gtag--gaattgtttgggttctcagtaggatttataaacatgcatggttaagcatttgtttgcttttgacatcttgtacaataattgttatttatgagtcagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCC
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gtaatcaaatcatctgcatttcttttccattttaatttcgtatattgataaatttagaacttcct----catcctttt---ttattgtactgcata--ttagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC
upper sequence: GLYMA19G17660.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 7
-------------gtaggaattgtttgggttctcagtaggattt-ataaacatgcatggttaagcatttgtttgcttttgacatcttgtacaataattgttatttatgagtcagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCC
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gtacttatacttatttaaacttcaacagttcttcacttcttcctgatcttagttcataggtacataaattctagaacactgtgatacatatcatttttttttgctgtgcattagATATCTTGTCCTTGCCAATATGTTGATGGAGTCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
upper sequence: GLYMA19G17660.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 7
gtaggaattgtttgggttctcagtaggatttataaacatgcatggttaagcatttgtttgc-ttttgacatcttgtacaataattgttatt--tatgagtcagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCC
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gtat-actcatctatact-tcatttctttctgtacagaagttt--tagaacactctaatacatatcgataaatatatttttggttttttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC
upper sequence: GLYMA19G17660.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------gtaggaattgtttgggttctcagtaggatttataaacatgcatggttaagcatttgtttgcttttgacatcttgtacaataattgttat-ttatgagtcagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCC
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gtatgctatggcttgggaagttgaattatttactcgtcttttatatgtctattttgaaagattcataagcatatttttataatcattttggtactattgtttgacactggatctatttctgcaccacctgatagATACTTGGTTCTGGCTAACATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCC
upper sequence: GLYMA19G17660.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------gtaggaattgtttgggttctcagt-------aggatttataaacatgcatggttaagcatttgtttgcttttgac----atcttgtacaataattgttatttatgagt-cagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCC
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gtgagtttgtttggtacgcttaaagtttcttgtatcatgagtttgtttggagtttcagtaaca-acttcctgaagcatactcttctgagtgacgagaactttgttaacaaggttttggatgggattgcagGTACCTGGTACTTGCTAACATGTTGATGGAGTCTGAAGTGAACCCATTTGATGCTCAGGAGGCTAAACCMapped 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|15285921|gb|BI469812.1|BI469812EST: TTCAAGAATTATGATGAAGCTGGTAGTCAGAGACGTATCCAATGTTTGAA ATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGA
genomic: TTCAAGAATTATGATGAAGCTGGTAGTCAGAGACGTATCCAATGTTTGAAgtaggtgaag ... tatgagtcagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagcatttgtttgcttttgacatcttgtacaataattgttatttatgagtcagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCC
ttttgac putative branch site (score: 3)
ttgtacaataattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggaattgtttgggttctcagtaggatttataaacatgcatggttaagcatttgtttgcttttgacatcttgtacaataattgttatttatgagtcagATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA