Sequence
atgc intronic sequence ATGC exonic sequence...tgacttcatctcttctactgatactttattttcttctttgtaaatacacgcataattctctctttctgatgtgacactcgatcgtgcattatttatgtagGTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGGATCATTGGCCCAATTGATCAAGGTTTGCTTGCTAAAGGACGGGATACAT
Basic information
species | Glycine max |
transcript | GLYMA09G29970.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 5
tgacttcatctcttc-tactgatactttattttcttctttgtaaatacac-gcataattctctctttctgatgtgacactcgatcgtgcattatttatgtagGTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGGATCATTGGCCCAATTGATCAAGGTTTGCTTGCTAAAGGACGGGATACAT
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tgatcttagcaggcaatgtttgcaatttatctatttactgttatacatagagaatgaatatgttagttcatcttgattcaccatggtctatgctcttc--agGTTCTTTTCCAAAATGATTCTCCTGCAACTTTACTTGCACGTGTGATGGGCATCATTGGTTCGATAGAACAAGCTATGCTTGCACAGGGACGTGAAACAT
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 5
tgacttcatctcttctactgatac--tttattttcttctttgtaaatacacgcataattctctctttctgatgtgacactcgatcgtgcattat-ttatgtagGTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGGATCATTGGCCCAATTGATCAAGGTTTGCTTGCTAAAGGACGGGATACAT
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gaaggtggtgattagaagctatgcagcttgctattttttttgttgttatacgcttg-tatggtggacggaagctgatgtgtg--cgtcctctatgcttttcagGTTCTTTTCCAAAACGATTCGCCTGCAACATTACTTGCTCGTGTGATGGGCATCATTGGCGCCATAGAACAAGCTATGCTTGCACAGGGACGGGACACCT
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 5
--tgacttcatctcttctactgatactttattttcttctttgtaaatacacgcataattctctctttctgatgtgacactcgatcgtgcattat-ttatgtagGTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGGATCATTGGCCCAATTGATCAAGGTTTGCTTGCTAAAGGACGGGATACAT
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ttttttattattatttcaaggtatatattttttacctattttctgtcatatgcttg-tatggtgcatggaagctgatgagtg--cgtcctctatgcttttcagGTCCTTTTCCAAAATGATTCTCCTGCAACATTACTTGCTCGCGTGATGGGCATCATTGGCTCCATAGAACAAGCTATGCTTGCACAGGGACGCGACACCT
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 11
-tgacttcatctcttctactgatactttattttcttctttgtaaata-cacgcataattctctctttctgatgtgacactcgatcgtgcattatttatgtagGTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGGATCATTGGCCCAATTGATCAAGGTTTGCTTGCTAAAGGACGGGATACAT
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agcaagatatcttacctggtttaatgtggtcattttccttaaaactatcaattatgattcctggtgcaaagcgctttacataaa-gtttgctatgttt-tagGTCCTCTTCCAAAATGATTCACCAGCGACGTTACTTGCACGGGTGATTGGAATAATAGGTTCAATTGACCAAGGCATGCTTGCTAAAGGACGTGATACATMapped 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|17963708|gb|BM270454.1|BM270454EST: TTGACATCTGGTCACTTGGATGCATCTTGGCAGAACTTTGTACTGGCAAT GTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGG
genomic: TTGACATCTGGTCACTTGGATGCATCTTGGCAGAACTTTGTACTGGCAATgtatgatcaa ... atttatgtagGTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGG
EST:
gi|151404434|gb|EV274248.1|EV274248EST: TTGACATCTGGTCACTTGGATGCATCTTGGCAGAACTTTGTACTGGCAAT GTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGG
genomic: TTGACATCTGGTCACTTGGATGCATCTTGGCAGAACTTTGTACTGGCAATgtatgatcaa ... atttatgtagGTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacgcataattctctctttctgatgtgacactcgatcgtgcattatttatgtagGTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGGATCATTGGCCCAATTGATCAAGGTTTGCTTGCTAAAGGACGGGATACAT
ttctgat putative branch site (score: 3)
attatttatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgacttcatctcttctactgatactttattttcttctttgtaaatacacgcataattctctctttctgatgtgacactcgatcgtgcattatttatgtagGTTCTCTTCCAAAATGATTCCCCTGCGACATTACTTGCTCGGGTGATTGGGATCATTGGCCCAATTGATCAAGGTTTGCTTGCTAAAGGACGGGATACAT
-gacttca
- - - - - - -tctactg
- - - - - - - - - - - - - - - - - - - - - - tacacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgtgcat