Sequence
atgc intronic sequence ATGC exonic sequencegtatggaagattattaaattttcatactttattccctatgtcaaactgccttctgaaattaatgagtttggtacttgcagGACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG
Basic information
species | Glycine max |
transcript | GLYMA13G00980.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 11
gtatggaagattattaa----attttcatactttattccc---tatgtcaaactgcct-tctgaaattaatgagtttggt-acttgcagGACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG
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gtatgggaatttgatgggatgatgcaagtggattatttacagataaatctagttctctatgttagattta-gagttaattgatttgcagGATGTCTTTGATTTGCCGTTCCACATGGCTAGAGATCAAATAGAAGAAAGTCTCAGAAATAAGATGACCTCTATAAAG
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S145_44V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------------------------------------------------------------------------------gtatggaag-attattaaattttcatactttattccctatgtcaaactgccttctgaaattaatgagtttggtacttgcagGACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG
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gtaattttcatgtgtactttgccttcaagctcatgtaagtttcagttgctgaatttcctgctcttgagactggtaaaataatcagttgtagacatgtcctgtgtctggctgtacaggcaaaagtttagatgcgaagctttcaatcattcacttcaccaaactgaattgatgcacttggtgcagGATGTATTTGACCTACCGTTTCACATGGCTAGAGATCAAATTGAACAAAGTTTACGTGCTAAAATGTCTATTATCAAG
upper sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S47_178V6.2 (Physcomitrella patens), 3'ss of exon 11
----------------------------------------------------------------------------------gtatggaagattattaaattttcatactttattccctat-gtcaaactgccttctgaaattaatgagtttggtac----ttgcagGACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG
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gtaatttcaaatcatattttgttttcaagtttcactcgcttagcgatcagaatgtggtgtaagaatcactttgcaacgtgttctgccccaggcagtacaagttcaagtgaaggtagccagtcatcaaccagccacttcactgagttgaattttatgcatttttacagGATGTATTTGACCTACCTTTTCATATGGCAAGAGATCAAATTGAACAAAGTTTGCGTGCCAAGATGTCCACTATTAAGMapped 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|10236681|gb|BE805569.1|BE805569EST: GAGTTGAAAGTGATCCTTCACAATCTCCATTGGTTGGGAAAATG GACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGT
genomic: GAGTTGAAAGTGATCCTTCACAATCTCCATTGGTTGGGAAAATGgtatggaaga ... gtacttgcagGACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGT
EST:
gi|51344846|gb|CO985579.1|CO985579EST: ATGAAAGAGTTGAAAGTGATCCTTCACAATCTCCATTGGTTGGGAAAATG GACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGT
genomic: ATGAAAGAGTTGAAAGTGATCCTTCACAATCTCCATTGGTTGGGAAAATGgtatggaaga ... gtacttgcagGACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttattccctatgtcaaactgccttctgaaattaatgagtttggtacttgcagGACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG
aattaat putative branch site (score: 3)
aaattaatgagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggaagattattaaattttcatactttattccctatgtcaaactgccttctgaaattaatgagtttggtacttgcagGACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA