Sequence
atgc intronic sequence ATGC exonic sequence...gtgtgtgcttacttcggagcatggctttctgaaaaacattctagtttgacgaaagagtttgctactggcattttaacattgaatgttgaaatttgaacagGGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGATGCGATTCGGAAG
Basic information
species | Glycine max |
transcript | GLYMA20G28970.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 16
-------------------------------------------------------------------------------------------gtgtgtgcttacttcggagcatg-gctttctgaaaaacat-tctagtttgacgaaagagtttgctactggcattt----taacattg--aatgttgaaatttgaacagGGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGATGCGATTCGGAAG
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gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 16
gtgtgtgcttacttcggagcatggctttctgaaaaacattctagtttgacgaaagagtttgctactggcattttaacattgaatgttgaa--atttgaacagGGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGATGCGATTCGGAAG
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------------------gtaagtctctctttgct-catttaagtaaaagaattatatctaaaacccacaatt-agttctcatggttgttttattcgcgcagTGATGGAGTAAGCGAAGGGCAATTCTATCAAGTTTTACTCTATGAGTTGGATGCAATTCGAAAG
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 14
--------gtgtgtgcttacttcggagcatggctttctgaaaaacattctagtttgacgaaagagtttgctactggcattttaacattgaatgttgaaatttgaacagGGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGATGCGATTCGGAAG
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ggatctctatgtgcagtgtcctcacaa-attactgcatgtgcatcattaagctcttttcatag---ttacaattcttatcctga--tcagatatt--aatttgagcagGGATGGTGTTAGTGAAGGGCAATTTTATCAAGTGCTACTTTATGAACTAGATGCAATCCGGAAAMapped 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|24205882|gb|BU965135.1|BU965135EST: TCCTTTAGAAAGGCAACAGGACAAAAGCCACTACGAATTATATTTTACAG GGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGA
genomic: TCCTTTAGAAAGGCAACAGGACAAAAGCCACTACGAATTATATTTTACAGgtcattatgt ... atttgaacagGGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGA
EST:
gi|19347375|gb|BM892255.1|BM892255EST: TCCTTTAGAAAGGCAACAGGACAAAAGCCACTACGAATTATATTTTACAG GGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGA
genomic: TCCTTTAGAAAGGCAACAGGACAAAAGCCACTACGAATTATATTTTACAGgtcattatgt ... atttgaacagGGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgacgaaagagtttgctactggcattttaacattgaatgttgaaatttgaacagGGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGATGCGATTCGGAAG
ttttaac putative branch site (score: 2)
attttaacattgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtgcttacttcggagcatggctttctgaaaaacattctagtttgacgaaagagtttgctactggcattttaacattgaatgttgaaatttgaacagGGACGGTGTAAGTGAAGGGCAATTTTACCAAGTTTTACTTTATGAGTTGGATGCGATTCGGAAG
gtgtgtg
- - - - - - - - - gcatggc
- - - - - - - - - - - - - - - -aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgt