Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttgctgtctttgtaaagtctcttaattctttgtattttagtgattgcaactcttgctcctaacattcttcattcatttcagGAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGCGAAATATATCAAGATGCAGATGAGGATACAAGAAGAGCAATGAAAAAGT
Basic information
species | Glycine max |
transcript | GLYMA09G23980.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 8
-----------gtatgtttgctgtctttgtaaagtctcttaa--ttctttgtattttagtgattgcaactcttgctcctaacattcttcattcatttcagGAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGCGAAATATATCAAGATGCAGATGAGGATACAAGAAGAGCAATGAAAAAGT
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gttagtatgatgcacatggttcaacgtttcactgcctgtggacattccttgaactctggtaatta----ttgaattgccatgactttgaatttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGTGACATCTACAGTGATGCTGATGAAGACATGCGACGAGCAATGATGAAAT
upper sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 8
---------gtatgtttgctgtctttgtaaagtctcttaattctttgtattttagtgattgcaactc---ttgctcctaacattcttcattcatttcagGAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGCGAAATATATCAAGATGCAGATGAGGATACAAGAAGAGCAATGAAAAAGT
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gtttgatgaagatcctcact-tatatatgtatcgatcttattgctagaacttgggtttatcgaatatgaatggggtttcatgatttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT
upper sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 8
gtatgtttgctgtctttgtaaagtctctta-attctttgtattttagtgattgcaactctt--gctcctaacattcttcattc--atttcagGAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGCGAAATATATCAAGATGCAGATGAGGATACAAGAAGAGCAATGAAAAAGT
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----gtttgatcaagatgcccacttttaggcatcacttttacttcagcaacttgggtttctcaaatatgaacggtgtttgtgtcggcaacagGAGAAGGAAGAAAAACTTGAAGGTGATGCTGCATTGAACAAGTTCTTCCGTGATATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGGACAAGT
upper sequence: GLYMA09G23980.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------gtatgtttgctgtctttgtaaagtctcttaattctttgtattttagtgattgcaactcttgctcctaacattcttcattc--atttcagGAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGCGAAATATATCAAGATGCAGATGAGGATACAAGAAGAGCAATGAAAAAGT
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gtttgcctgcaatctagatcctgttactttggttttcattattgtttaacatcata-tgagaacctgaggaattttatttgggggtcaactctttggtggtttgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAAATTTTTCCGGGACATATATAAAGATGCAGACGAAGACACAAGAAGGGCCATGCAAAAATMapped 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|254347816|gb|GR854065.1|GR854065EST: CAAAACAAACAAGAGATTGGGACAAGATTGAAGCTCAAGTCAAGAAAGAG GAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGC
genomic: CAAAACAAACAAGAGATTGGGACAAGATTGAAGCTCAAGTCAAGAAAGAGgtatgtttgc ... ttcatttcagGAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgtattttagtgattgcaactcttgctcctaacattcttcattcatttcagGAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGCGAAATATATCAAGATGCAGATGAGGATACAAGAAGAGCAATGAAAAAGT
tcctaac putative branch site (score: 1)
ttcttcattcatttc CT-rich tract
tattttagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttgctgtctttgtaaagtctcttaattctttgtattttagtgattgcaactcttgctcctaacattcttcattcatttcagGAGAAAGATGAAAAGCTTGATGGCGATGCTGCATTGAACAAATTTTTCCGCGAAATATATCAAGATGCAGATGAGGATACAAGAAGAGCAATGAAAAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA