Sequence
atgc intronic sequence ATGC exonic sequencegtttcttctttgttagagttgcctattacatttaaaagatgattgactagagtagctgataatgcatctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG
Basic information
species | Glycine max |
transcript | GLYMA02G35640.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
------------------gtttct-tctttgt-tagagttgcctattacatttaaaagatgattgactagagtagctgataatgcatctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG
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gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
upper sequence: GLYMA02G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G173428_T04 (Zea mays), 3'ss of exon 5
-----gtttcttctttgttagagttgccta--ttacatttaaaag--atgattgactagagtagctgataatgcatctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG----------------------------------------
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gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgcc------atttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGGTTCCCTACCTACACTCATGCTATACCACTAGGTGTTCAT
upper sequence: GLYMA02G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G161649_T01 (Zea mays), 3'ss of exon 3
gtttcttctttgttagagttgcc-tattacatttaaaagatgattgactagagtagctgataat-----gcat-ctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG
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gtatgcaaccttcaggaatcaacatactttgttttaa-gttcatggctcaaggttcatgcttgtttctggtatgctctttaaaaagagtt-tggcatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG
upper sequence: GLYMA02G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G036634_T01 (Zea mays), 3'ss of exon 14
gtttcttctttgttagagttgcc-tattacatttaaaagatgattgactagagtagctgataat-----gcatctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG
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gtatgcaaccttcaggaatcaacatactttgttttaa-gttcatggctcaaggttcatgcttgtttctggtatgctctttaaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG
upper sequence: GLYMA02G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G132286_T01 (Zea mays), 3'ss of exon 4
gtttcttctttgttagagttgcc-tattacatttaaaagatgattgactagagtagctgataat-----gcat-ctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG
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gtatgcaaccttcaggaatcaacatactttgttttaa-gttcatggctcaaggttcatgcttgtttctggtatgctctttaaaaaaaagtttgccatttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG
upper sequence: GLYMA02G35640.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 4
-----gtttcttctttgttagagttgcctat--tacatttaaaag--atgattgactagagtagctgataatgcatctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG
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gtatgcaaccttcaggaatcaacatacttgtgttaagttcatagcccaaggttcattcttgtatctggtatggtatttaaaaaagtttgcc------atttttctgtgatctgcagTCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagctgataatgcatctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG
atctaat putative branch site (score: 3)
tatttctc putative PPT
tatatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcttctttgttagagttgcctattacatttaaaagatgattgactagagtagctgataatgcatctctttggtctgacctatctaatggtgctatatttctcagTCTGAAGATGAAAGGGAGATGTGTTCAAGAACAATTTATTGCACAAATATTGACAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG