Sequence
atgc intronic sequence ATGC exonic sequence...cttttgttatttctttcctcatcatagcaaaggccaagaagaatctaaatgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
Basic information
species | Glycine max |
transcript | GLYMA17G01900.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 4
----cttttgttatttctttcctcatcatagcaaaggccaa--gaagaatctaa--atgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
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aacttttcaattatcccttgttatttgatcgtactattctactgaaaaacctcatcatgctccttacat----aattt--taatgcat--cgtgctatcgttttgtagGATGCCAAAGCTAAAGACATCGATGATGTGCTGATTCTTTCTGGTGATCATCTCTACCGCATGGACTACATGGACTTTGTTCAG
upper sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
-cttttgttatttct--ttcctcatcatagcaaaggccaagaagaatctaaatgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
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ttcaaagggactgccagttccctattgctttactttgtaatattattataa-taccacaaagctgttccttgaagaaat-tgtaataca-taatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG
upper sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 4
cttttgttatttctttcctcatcatagcaaaggccaagaagaatctaaatgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
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--------------------------gtagaaatcagacttaaactagcttatcatc--acatcaatagacaagcggtccaacattctttt----catagGATGCAAGAAGCAAGGACATAGAGGATGTATTGATCCTTTCTGGAGATCACCTCTACAGGATGGATTACATGGATTTTATACAG
upper sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 4
cttttgttatttctttcctcatcatagcaaaggccaagaagaatctaaatgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
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------gtacccatatttcacttctagttaggattctggggtaaccaa----tagacgg-tatcaaaccaagaagggtgttaaagcttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG
upper sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 5
cttttgttatttctttcctcatcatagcaaaggccaagaagaatctaaatgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgta-gGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
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--------------------------------------gtactctttaccatttccaaggtgttgggc-tcgtatgctgaggtttcgttttgtatgacaagGATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAG
upper sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ25399 (Selaginella moellendorffii), 3'ss of exon 4
cttttgttatttctttcctcatcatagcaaaggccaagaagaatctaaatgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgta-gGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
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---------------------------------------gtactcttaccatttccaaggtgttggac-tcgcatgctgaggtttcgttttgtatgacaagGATGTGAGAAACAAGGACGTCGACTACGTGCTTGTTCTCTCCGGTGATCACCTCTACCGCATGGACTACATGGACTTTGTCCAGMapped 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|13125839|gb|BG316409.1|BG316409EST: GGTTTCAAGGTACTGCTGATGCAGTGAGGCAGTTTCACTGGCTCTTTGAG GATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCAC
genomic: GGTTTCAAGGTACTGCTGATGCAGTGAGGCAGTTTCACTGGCTCTTTGAGgtattaagtc ... tatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCAC
EST:
gi|20449568|gb|BQ253692.1|BQ253692EST: GGTTTCAAGGTACTGCTGATGCAGTGAGGCAGTTTCACTGGCTCTTTGAG GATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGACCAC
genomic: GGTTTCAAGGTACTGCTGATGCAGTGAGGCAGTTTCACTGGCTCTTTGAGgtattaagtc ... tatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaatgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
atctaaa putative branch site (score: 3)
tgcttct putative PPT
atgttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttgttatttctttcctcatcatagcaaaggccaagaagaatctaaatgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - -ccaagaa
- - - - - - - - - - - - - - - - - - - - - - -taaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctt