Sequence
atgc intronic sequence ATGC exonic sequencegtaagtattattaatatgctttttatgtaatgctacaaaagactaatgcacagaaataatttccttatacagGTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCTGTTTTTCTGCATGGGATCCTAGGTTGCAGGAAAAACTGGG
Basic information
species | Glycine max |
transcript | GLYMA11G01670.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g66240.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------gtaagtattattaatatgctttttatgtaatgctacaaaa-gactaatgcacagaaataatttccttatacagGTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCTGTTTTTCTGCATGGGATCCTAGGTTGCAGGAAAAACTGGG
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gtacgtattgcattcatacgaactcagtgacatgtcactagttgttaaataatgttagctagaagttaaatggtcaa-atgttatggtgtaagacaagctattcatagccatcacttcacct--cagGTGCAATGGAACTCATTTATGGACAAATCAGTACCTGATCCACCAACAGCTGTTCTCCTTCATGGCATCCTTGGGAGCAGGAAAAACTGGG
upper sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007160_T02 (Zea mays), 3'ss of exon 3
----------------------------------gtaagtattattaatatgctttttatgtaatgctacaaaagactaatgcacagaaataatttcctta--tacagGTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCTGTTTTTCTGCATGGGATCCTAGGTTGCAGGAAAAACTGGG
||| | || || |||| || | | | ||| ||| || | || | | | ||| | ||||| ||||| ||| ||||||||| ||| ||||||| |||||||| |||||| |||| ||||| ||||| || |||||||||||||||
gtaagttttgcattcacgcaaattatctgtcattagttgtaaaactagcttgattttgatttttttgtccaatcgac--ataaatcaaattcaacactttaacttcagGTTCAGTGGAATTCATTTATGGACAAATCAATACCTGATCCACCAACAGCTGTTCTTCTTCATGGCATCCTTGGGAGCAGGAAAAACTGGG
upper sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G007160_T03 (Zea mays), 3'ss of exon 3
----------------------------------gtaagtattattaatatgctttttatgtaatgctacaaaagactaatgcacagaaataatttcctta--tacagGTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCTGTTTTTCTGCATGGGATCCTAGGTTGCAGGAAAAACTGGG---------
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gtaagttttgcattcacgcaaattatctgtcattagttgtaaaactagcttgattttgatttttttgtccaatcgac--ataaatcaaattcaacactttaacttcagGTTCAGTGGAATTCATTTATGGACAAATCAATACCTGATCCACCAACAGCTGTTCTTCTTCATGGCATCCTTGGGAGCAGGAAAAACTGGGGTAAATGAGMapped 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|213599045|gb|DB972003.1|DB972003EST: GCATATGATTTGATTCAGGGGGCACTT GTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCT
genomic: GCATATGATTTGATTCAGGGGGCACTTgtaagtatta ... ccttatacagGTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCT
EST:
gi|213592508|gb|DB971650.1|DB971650EST: GCATATGATTTGATTCAGGGGGCACTT GTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCT
genomic: GCATATGATTTGATTCAGGGGGCACTTgtaagtatta ... ccttatacagGTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCT
EST:
gi|31561071|gb|CD486909.1|CD486909EST: GCATATGATTTGATTCAGGGGGCACTT GTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCT
genomic: GCATATGATTTGATTCAGGGGGCACTTgtaagtatta ... ccttatacagGTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttttatgtaatgctacaaaagactaatgcacagaaataatttccttatacagGTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCTGTTTTTCTGCATGGGATCCTAGGTTGCAGGAAAAACTGGG
gactaat putative branch site (score: 2)
tttccttat putative PPT
aaataatttccttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtattattaatatgctttttatgtaatgctacaaaagactaatgcacagaaataatttccttatacagGTAAGGTGGAGTTCTGTTATGGACAGATCTTTACCTGAGCCACCAACGGCTGTTTTTCTGCATGGGATCCTAGGTTGCAGGAAAAACTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT