Sequence
atgc intronic sequence ATGC exonic sequence...catcccatgctcatctatccaggcaccacaatatggtgtagatggctttctaagacctatgagaactaaccaattgtgtttcttgttttttttttaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
Basic information
species | Glycine max |
transcript | GLYMA17G12060.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G12060.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g07230.1 (Oryza sativa), 3'ss of exon 5
-catcccatgctcatctatccaggcaccacaatatggtgtagatggctttctaagacctatgagaactaaccaattgtgtttcttgttttttttttaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
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taaaataataaaaacaaagtaatgtcaaacatcagattatacttctccctctgagaaacaagcatacatgttcaagatctcattaaagtacacttt-tcagGACACTTGACATCCAAGAGCGATGTATATAGCTTCGGAGTAGTGTTACTCGAGATGTTAACCGGTAGACGATCAATGGACAAGAAGCGGCCTACTGGGGA
upper sequence: GLYMA17G12060.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G007801_T01 (Zea mays), 3'ss of exon 2
catcccatgctcatctatccaggcaccacaatatggtg--tagatgg--ctttctaagacctatgagaactaaccaattgtgtttcttgttttttttttac----cagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
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-------tgaaaactgaaaaacataacaaaaagtgttagtttaacgattctttctttaagcagttgata-tgtcaagttttgttactcatgttatgcatattgttcagGGCACTTGACATCTAAGAGTGATGTTTATAGCTTCGGAGTTGTGCTACTCGAGATGTTGACTGGGAGAAGATCAATGGACAAGAAGCGGCCTACGGGGGA
upper sequence: GLYMA17G12060.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g05720.t01 (Vitis vinifera), 3'ss of exon 5
--catcccatgctcatctatccaggcaccacaatatggtgtagatggctttctaagacctatgagaactaaccaattgtgtttcttgttttttttttaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
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gacatctaagagcaatgctctcaaatat-gtgttgttccattcctttgaacttgaaaaatttgacaccttacctgt-acaattttggctctttttctcttagGACACTTGACATCTAAGAGCGATGTTTACAGCTTTGGGGTTGTGCTACTTGAGATTTTAACTGGTAGAAGATCAATGGACAAGAAACGCCCTCGCGGAGA
upper sequence: GLYMA17G12060.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ22709 (Selaginella moellendorffii), 3'ss of exon 5
catcccatgctcatctatccaggcaccacaatatggtgtagatggctttctaagacctatgagaactaaccaattgtgtttcttgttttttttttaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
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---------------------gtaagttcacaaagaaagaaaaaaaattgagagttct-tgaacttaaaaggatcgtacct-ttgtttcct-----ccagGTCACTTGACAGCCAGGAGCGATGTTTACAGCTTTGGAGTTGTCTTCCTGGAGATGCTAACTGGCAGACGATCCATGGACAAGTCTAGACCCACTGGCGA
upper sequence: GLYMA17G12060.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ19239 (Selaginella moellendorffii), 3'ss of exon 5
catcccatgctcatctatccaggcaccacaatatggtgtagatggctttctaagacctatgagaactaaccaattgtgtttcttgttttttttttaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
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----------------------gtaagttcacaaggaaagaaaaaaacttgagagttcttgaacttaaaaggatcgtacct-ttgtttcct-----ccagGTCACTTGACAGCCAGGAGCGATGTTTACAGCTTTGGAGTTGTCTTCCTGGAGATGCTAACTGGCAGACGATCCATGGACAAGTCTAGACCCACTGGAGAMapped 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|10232151|gb|BE801039.1|BE801039EST: CAGGGTAGTTGGAACTTATGGTTATGCTGCTCCAGAATATGTCATGACAG GACACTTGACAGCTAAAAGTGATGTTTATAGCTNTGGAGTTGTGTTACTTG
genomic: CAGGGTAGTTGGAACTTATGGTTATGCTGCTCCAGAATATGTCATGACAGgtaagaatgt ... tttttaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctaagacctatgagaactaaccaattgtgtttcttgttttttttttaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
aactaac putative branch site (score: 1)
ttgtgtttcttgtttt putative PPT
tttcttgttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catcccatgctcatctatccaggcaccacaatatggtgtagatggctttctaagacctatgagaactaaccaattgtgtttcttgttttttttttaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - -catgctc
- - - - - - - - - - - -caccaca
- - - - - - - - - - - - - - - -tatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cctatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaacca