Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgtatctttcttttttattggagccactacttgcattgtgggagattgaaaacaacaagaaggattttgaactgtgagagtattgacaaaacattgcaatttataaatatggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACAATCTCA
Basic information
species | Glycine max |
transcript | GLYMA20G33910.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 5
gtttgtgtatctttcttttttattggagccactacttgcattgtgggagattgaaaacaacaagaaggattttgaactgtg--agagtattgacaaaacattgcaa--tttataaatatggtg---------atagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACAATCTCA
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---------------------------gtaactgctgatctgcaatgagttagaaagctgtgtcatgttttttcctctcttctcagttctctctaagacactccatgctttatatattcattattctcttttatagGTTGGTACTATATCAGCTAATGGGGAAAGGGAAATTGGTGAGCTCATTGCAAAAGCTATGGAGAAGGTTGGCAAAGAGGGAGTCATCACTATTACG
upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 5
gtttgtgtatctttcttttttattggagccactacttgcattgtgggagattgaaaacaacaagaaggattttgaactgtgag--agtattgacaaaacattgcaat-ttataaatatggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACAATCTCA
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----------------------------gtaatacttgtgattc-----attgcagatctcattatgtgttt-gacttgtttcttaatcttaatctgttactaagttcttatgttcatatataaagGTGGGCACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCAAAGGCTATGGAGAAGGTTGGCAAGGAGGGTGTAATCACCATTGCG
upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 4
gtttgtgtatctttcttttttattggagccactacttgcattgtgggagattgaaaacaacaagaaggattttgaactgtgagagtattgacaaaacattgcaatttataaatatggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACAATCTCA
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------------------------------------------------------gtatatctgcaaggctctagttttatgttcccttcatctttttaaaattctttctctatcctgtga-agGTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG
upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 4
gtttgtgtatctttcttttttattggagccactacttgcat-tgtgggagattgaaaacaacaagaaggattttgaactgtgagagtattgacaaaacattgcaatttataaa-tatggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACAATCTCA
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-----------------------------------gtatatctgcagcaccctagttactttattttgt-tcttatcctgtcc-atccctcacctttttttattctctctatcctgtatgtaaagGTGGGTACAATATCAGCAAATGGAGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG
upper sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 5
---------------------------gtttgtgtatctttcttttttattggagccactacttgcattgtgggagat----tgaaaacaacaagaaggattttgaactgtgagagtattgacaaaacattgcaa---tttata-aatatggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACAATCTCA
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gtaagcaaatcaccatctgaaggtgatactagaattttagcatcttgtttttgggcttaaactc-taatatagaaaatctcgtggatgtgttgccgaagctact-aatggaagtcacttcaacggatcattccttgcttttgtgtggtgttctgccagGTTGGAACAATCTCTGCGAATGGAGACCGAGAAATTGGTGACTTGCTAGCTCGTGCTATGGAGAAGGTTGGCAAGGAGGGTGTCATCACTGTCTCTMapped 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|16277971|gb|BI942659.1|BI942659EST: ATCTGAAAAGCAGAGCACGTATGATTAGCACTTCTGAAGAAATTGCCCAG GTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCA
genomic: ATCTGAAAAGCAGAGCACGTATGATTAGCACTTCTGAAGAAATTGCCCAGgtttgtgtat ... atggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCA
EST:
gi|209725419|gb|BW658281.1|BW658281EST: ATCTGAAAAGCAGAGCACGTATGATTAGCACTTCTGAAGAAATTGCCCAG GTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCA
genomic: ATCTGAAAAGCAGAGCACGTATGATTAGCACTTCTGAAGAAATTGCCCAGgtttgtgtat ... atggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgaactgtgagagtattgacaaaacattgcaatttataaatatggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACAATCTCA
tattgac putative branch site (score: 2)
aaaacattgcaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgtatctttcttttttattggagccactacttgcattgtgggagattgaaaacaacaagaaggattttgaactgtgagagtattgacaaaacattgcaatttataaatatggtgatagGTTGGAACAATATCTGCCAATGGGGAGAGGGAAATTGGTGAGTTAATTGCAAAAGCTATGGAGAAAGTTGGCAAAGAGGGTGTCATCACAATCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG