Sequence
atgc intronic sequence ATGC exonic sequencegtaaacattggccttcattctgtatcttgagttattgaaattttcctgctctgatgtatatttttgcttattatttatttatttatttattttttttggggggggggggggggggttctgactctagTTACTCAGAGTCTGAATACTTCAAGCAAACAATGCGCCAAGGTGGTCTTACTAAACCAAAAGAGCCTCGTATTCCTAGGATGCCTCAATT
Basic information
species | Glycine max |
transcript | GLYMA17G02640.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 16
gtaaacattggccttcattctgtatcttgagttattgaaattttcctgctctgatgtatatttttgcttattatttatttatttatttattt--tttttggggggggggggggggggttctgactctagTTACTCAGAGTCTGAATACTTCAAGCAAACAATGCGCCAAGGTGGTCTTACTAAACCAAAAGAGCCTCGTATTCCTAGGATGCCTCAATT
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-------------------------------------------------------gtaagtctctatct-ctatgtgtgcatgcacacgtctggtgctcaaactgacctaattttgtttgttactctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCGCACCT
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 16
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 16
gtaaacattggccttcattctgtatcttgagttattgaaattttcctgctctgatgtatatttttgcttattatttatttatttatttattt--tttttggggggggggggggggggttctgactctagTTACTCAGAGTCTGAATACTTCAAGCAAACAATGCGCCAAGGTGGTCTTACTAAACCAAAAGAGCCTCGTATTCCTAGGATGCCTCAATT
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-------------------------------------------------------gtaaatctctatct-ctatgtgtgcatgcacacgtctggtgctgaaactgacctaattttgtttgttactctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT
upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 16
gtaaacattggccttcattctgtatcttgagttattgaaattttcctgctctgatgt-atatttttgcttattatttatt-tatttatttattttttttggggggggggggggggggttctgactctagTTACTCAGAGTCTGAATACTTCAAGCAAACAATGCGCCAAGGTGGTCTTACTAAACCAAAAGAGCCTCGTATTCCTAGGATGCCTCAATT
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-------------gtaattgtgaattttcagttgccaa----cttatgttataattttatgtttttcattatcatttaagacatgtttccattttctt------------------gtcctttaagtagTTACTCAGAGTCTGAATACTTTAAGCAAACAATGCGGCAAGGTGCTCCAGCAAAACAAAGAGAGCCTAGAATACCGCGCATGCCCCAGCTMapped 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|193455189|gb|FK419222.1|FK419222EST: ATTGTGAGTGAAAATTGGGTCGAGCCACCAAGAAGAGAACGGAAGCGCAA TTACTCAGAGTCTGAATACTTCAAGCAAACAATGCGCCGAGGTGGTCTTAC
genomic: ATTGTGAGTGAAAATTGGGTCGAGCCACCAAGAAGAGAACGGAAGCGCAAgtaaacattg ... ctgactctagTTACTCAGAGTCTGAATACTTCAAGCAAACAATGCGCCAAGGTGGTCTTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatttatttatttattttttttggggggggggggggggggttctgactctagTTACTCAGAGTCTGAATACTTCAAGCAAACAATGCGCCAAGGTGGTCTTACTAAACCAAAAGAGCCTCGTATTCCTAGGATGCCTCAATT
ttctgac putative branch site (score: 2)
tttatttatttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacattggccttcattctgtatcttgagttattgaaattttcctgctctgatgtatatttttgcttattatttatttatttatttattttttttggggggggggggggggggttctgactctagTTACTCAGAGTCTGAATACTTCAAGCAAACAATGCGCCAAGGTGGTCTTACTAAACCAAAAGAGCCTCGTATTCCTAGGATGCCTCAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG