Sequence
atgc intronic sequence ATGC exonic sequence...atagtttggattaactaaaggatcactcaattgctcatcctattcttttgttctttgaataattaatgttgttaaccctttctaacgaagtaattcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG
Basic information
species | Glycine max |
transcript | GLYMA20G33190.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G33190.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g01750.2 (Oryza sativa), 3'ss of exon 4
atagtttggattaactaa-aggatcactcaattgctcatcctattcttttgttctttgaataattaatgttgttaac-cctttctaacgaagtaattcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG
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--tttatggacaggcttgtactattcactaagcttttactggattactgtctatcattgatcactcctgagatcatttcctttttttctaaatcatttctagTGTTGACGTATAGACATGAGCTTGGAATGAACTACAATTTCATACGCCCAGACTTGATCGTGGGCTCCTGCTTACAG
upper sequence: GLYMA20G33190.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G052546_T01 (Zea mays), 3'ss of exon 4
-atagtttggattaactaaaggatcactcaattgctcatcctattcttttgttct-ttgaataattaatgttgttaaccctttctaacgaagtaattcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG
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tgtgcttgccatctaatttttg-tgattgcgttatgcttttagtaagtttggtctattaacttatctgatatgtgtttcttttccccccatgttatt-atagCGTTGACATATAGACATGAACTCGGGATGAACTACAATTTCATACGCCCAGACTTGATTGTAGGATCCTGCTTACAG
upper sequence: GLYMA20G33190.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 4
---atagtttggattaactaaaggatcactcaattgctcatcctattcttttgttctttgaataattaatgttg-ttaaccctttctaacgaagtaattcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG
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aacttaatgggaatgctctttaaaa--gtttccttttttgtcttgctttgtgttcatgcatatggttttagctaaccatttcattcttatgttctgat--acagTATTGACTTATAGGCATGAGCTAGGAATGAATTACAACTTCATTCGTCCAGACTTGATTGTGGGGTCTTGCCTACAGMapped 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|192321003|gb|FK013505.1|FK013505EST: AGAAAAGTCTGAGACATATAGTCATAGCATGACAGAAGCCATGGGTGCTG TTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAG
genomic: AGAAAAGTCTGAGACATATAGTCATAGCATGACAGAAGCCATGGGTGCTGgtatgtttaa ... taattcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAG
EST:
gi|13312616|gb|BG406267.1|BG406267EST: AGAAAAGTCTGAGACATATAGTCATAGCATGACAGAAGCCATGGGTGCTG TTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAG
genomic: AGAAAAGTCTGAGACATATAGTCATAGCATGACAGAAGCCATGGGTGCTGgtatgtttaa ... taattcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttctttgaataattaatgttgttaaccctttctaacgaagtaattcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG
ttctaac putative branch site (score: 1)
tttgaataattaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagtttggattaactaaaggatcactcaattgctcatcctattcttttgttctttgaataattaatgttgttaaccctttctaacgaagtaattcacagTTTTGACTTATAGGCATGAATTAGGAATGAACTATAATTTCATCCGTCCAGACTTGATTGTGGGATCATGCCTACAG
- - - - - - - - - - - tcactca
- - - - - - - - - - - - - - - - -ctcatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctttc