Sequence
atgc intronic sequence ATGC exonic sequence...aaatgttttcagttgaagtatcttgctgttgtttcgattttttcctggaaataataatcatgagattgcaacacctaataggagtaatttctgttggtagGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG
Basic information
species | Glycine max |
transcript | GLYMA17G01360.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 3
aaatgttttcagttgaa--gtatcttgctgttgtttcgattttttcctggaaataataatcatgagattgcaac-acctaataggagtaatttctgttggtagGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG
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---tgctgatggttaggtcgctgcatgaaatatacacacttttcctttttaaggggctctcttatttcaggtacgattttaattttgtttctctttttgatagGGTGGATTTGATATGATCTGCAGTGGTAGGGACAAGATTGAAACACCAGAGCAG
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 3
aaatgttttcagttgaagtatcttgctgttgtttcgattttttcctggaaataataatcatgagattgcaacacctaataggagtaatttctgttggtagGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG
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aaacttctttaacacacacacacacatatgacatatgtatgtatgtgtacacacacattatttccttttgatgatgcattaaaattttgtctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 3
aaatgttttcagt-tgaagtatcttgctgttgtttcgattttttcctggaaataataatcatgagattgcaacacctaataggagtaatt--tctgttggtagGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG
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-caaattttcatcatgaagagt--tggaactaaaagctttgttacttaaagatatgcattttgtgtttattcttagtagtttttgttgtgagtctctttgcagGGTGGATTTGATATGATATGTAGTGGAAGAGACAAGATTGAAACTCCAGAGCAG
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------aaatgttttcagttgaagtatcttgctgttgtttcgattttttcctggaaataataatcatgagattgcaacacctaataggagtaatt--tctgttggt------agGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG
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gtacttggattcagatccttccacaagatttgaatttacac-tccactagatgtggagcattagtccttggttaaatatacttgtctttttaagtcgatgtggttataattctttttttggtctcaacagGGTGGTTTTGACATGATCTGCAGTGGAAGAGACAAGATTGAAACACCTGACCAG
upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 3
--aaatgttttcagttgaagtatcttgctgttgtttcgattttttcctggaaataataatcatgagattgcaacacctaataggagtaatttctgttggtagGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG
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gcattcacgcacattttatctatgt-gctcatgtatgcacacaggcatgtga-taccaccaatatagcctcaacttgtattctttgtcttgttttatatcagGGTGGTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGMapped 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|254330861|gb|GR842126.1|GR842126EST: ATTTATCCTTACAGAAATCAG GGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAG
genomic: ATTTATCCTTACAGAAATCAGgtttattttt ... ctgttggtagGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaaataataatcatgagattgcaacacctaataggagtaatttctgttggtagGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG
acctaat putative branch site (score: 3)
tttctgtt putative PPT
ataataatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatgttttcagttgaagtatcttgctgttgtttcgattttttcctggaaataataatcatgagattgcaacacctaataggagtaatttctgttggtagGGTGGTTTTGACATGATTCGCAGTGGAAGGGACAAGATTGAAACTCCAGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - ggaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacacc